Dimensionless Analysis and Mathematical Modeling of Electromagnetic Levitation (EML) of Metals

NASA Astrophysics Data System (ADS)

Gao, Lei; Shi, Zhe; Li, Donghui; Yang, Yindong; Zhang, Guifang; McLean, Alexander; Chattopadhyay, Kinnor

2016-02-01

Electromagnetic levitation (EML), a contactless metal melting method, can be used to produce ultra-pure metals and alloys. In the EML process, the levitation force exerted on the droplet is of paramount importance and is affected by many parameters. In this paper, the relationship between levitation force and parameters affecting the levitation process were investigated by dimensionless analysis. The general formula developed by dimensionless analysis was tested and evaluated by numerical modeling. This technique can be employed to design levitation systems for a variety of materials.

A hemodynamic-based dimensionless parameter for predicting rupture of intracranial aneurysms

NASA Astrophysics Data System (ADS)

Asgharzadeh, Hafez; Varble, Nicole; Meng, Hui; Borazjani, Iman

2016-11-01

Rupture of an intracranial aneurysm (IA) is a disease with high rates of mortality. Given the risk associated with the aneurysm surgery, quantifying the likelihood of aneurysm rupture is essential. There are many risk factors that could be implicated in the rupture of an aneurysm. However, the hemodynamic factors are believed to be the most influential ones. Here, we carry out three-dimensional high resolution simulations on human subjects IAs to test a dimensionless number, denoted as An number, to classify the flow mode. An number is defined as the ratio of the time takes the parent artery flow transports through the expansion region to the time required for vortex formation. Furthermore, we investigate the correlation of IA flow mode and WSS/OSI on the human subject IAs. Finally, we test if An number can distinguish ruptured from unruptured IAs on a database containing 204 human subjects IAs. This work was supported by National Institute Of Health (NIH) Grant R03EB014860 and the Center of Computational Research (CCR) of University at Buffalo.

Estimating Mass of Inflatable Aerodynamic Decelerators Using Dimensionless Parameters

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

This paper describes a technique for estimating mass for inflatable aerodynamic decelerators. The technique uses dimensional analysis to identify a set of dimensionless parameters for inflation pressure, mass of inflation gas, and mass of flexible material. The dimensionless parameters enable scaling of an inflatable concept with geometry parameters (e.g., diameter), environmental conditions (e.g., dynamic pressure), inflation gas properties (e.g., molecular mass), and mass growth allowance. This technique is applicable for attached (e.g., tension cone, hypercone, and stacked toroid) and trailing inflatable aerodynamic decelerators. The technique uses simple engineering approximations that were developed by NASA in the 1960s and 1970s, as well as some recent important developments. The NASA Mars Entry and Descent Landing System Analysis (EDL-SA) project used this technique to estimate the masses of the inflatable concepts that were used in the analysis. The EDL-SA results compared well with two independent sets of high-fidelity finite element analyses.

A dimensionless parameter for classifying hemodynamics in intracranial

NASA Astrophysics Data System (ADS)

Asgharzadeh, Hafez; Borazjani, Iman

2015-11-01

Rupture of an intracranial aneurysm (IA) is a disease with high rates of mortality. Given the risk associated with the aneurysm surgery, quantifying the likelihood of aneurysm rupture is essential. There are many risk factors that could be implicated in the rupture of an aneurysm. However, the most important factors correlated to the IA rupture are hemodynamic factors such as wall shear stress (WSS) and oscillatory shear index (OSI) which are affected by the IA flows. Here, we carry out three-dimensional high resolution simulations on representative IA models with simple geometries to test a dimensionless number (first proposed by Le et al., ASME J Biomech Eng, 2010), denoted as An number, to classify the flow mode. An number is defined as the ratio of the time takes the parent artery flow transports across the IA neck to the time required for vortex ring formation. Based on the definition, the flow mode is vortex if An>1 and it is cavity if An<1. We show that the specific definition of Le et al. works for sidewall but needs to be modified for bifurcation aneurysms. In addition, we show that this classification works on three-dimensional geometries reconstructed from three-dimensional rotational angiography of human subjects. Furthermore, we verify the correlation of IA flow mode and WSS/OSI on the human subject IA. This work was supported partly by the NIH grant R03EB014860, and the computational resources were partly provided by CCR at UB. We thank Prof. Hui Meng and Dr. Jianping Xiang for providing us the database of aneurysms and helpful discussions.

Development of Dimensionless Index Assessing Low Impact Development in Urban Areas

NASA Astrophysics Data System (ADS)

Jun, S. H.; Lee, E. H.; Kim, J. H.

2017-12-01

Because the rapid urbanization and industrialization have increased the impervious area of watersheds, inundation in urban area and water pollution of river by non-point pollutants have caused serious problems for a long time. Low Impact Development (LID) techniques have been implemented for the solution of these problems due to its cost effectiveness for mitigating the water quality and quantity impact on urban areas. There have been many studies about the effectiveness of LID, but there is a lack of research on developing an index for the assessment of LID performance. In this study, the dimensionless reliability index of LID is proposed. The index is developed using Distance Measure Method (DMM). DMM is used to consider the parameters that have different units. The parameters for reliability of LID are the amount of pollutant at the outfall and the flooding volume. Both parameters become dimensionless index by DMM. Weighted factors in dimensionless index are considered to realize the behavior of reliability for the variation of importance to the parameters. LID is applied to an actual area called Gasan city in Seoul, South Korea where inundation is frequently occurred. The reliability is estimated for 16 different rainfall events. For each rainfall event, the parameters with LID installation are compared with those of no LID installation. Depending on which parameter is considered more important, the results showed difference. In conclusion, the optimal locations of LID are suggested as the weighted factors change.

Theoretical investigation of the upper and lower bounds of a generalized dimensionless bearing health indicator

NASA Astrophysics Data System (ADS)

Wang, Dong; Tsui, Kwok-Leung

2018-01-01

Bearing-supported shafts are widely used in various machines. Due to harsh working environments, bearing performance degrades over time. To prevent unexpected bearing failures and accidents, bearing performance degradation assessment becomes an emerging topic in recent years. Bearing performance degradation assessment aims to evaluate the current health condition of a bearing through a bearing health indicator. In the past years, many signal processing and data mining based methods were proposed to construct bearing health indicators. However, the upper and lower bounds of these bearing health indicators were not theoretically calculated and they strongly depended on historical bearing data including normal and failure data. Besides, most health indicators are dimensional, which connotes that these health indicators are prone to be affected by varying operating conditions, such as varying speeds and loads. In this paper, based on the principle of squared envelope analysis, we focus on theoretical investigation of bearing performance degradation assessment in the case of additive Gaussian noises, including distribution establishment of squared envelope, construction of a generalized dimensionless bearing health indicator, and mathematical calculation of the upper and lower bounds of the generalized dimensionless bearing health indicator. Then, analyses of simulated and real bearing run to failure data are used as two case studies to illustrate how the generalized dimensionless health indicator works and demonstrate its effectiveness in bearing performance degradation assessment. Results show that squared envelope follows a noncentral chi-square distribution and the upper and lower bounds of the generalized dimensionless health indicator can be mathematically established. Moreover, the generalized dimensionless health indicator is sensitive to an incipient bearing defect in the process of bearing performance degradation.

Summary of dimensionless Texas hyetographs and distribution of storm depth developed for Texas Department of Transportation research project 0–4194

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

2005-01-01

Hyetographs and storm depth distributions are important elements of hydraulic design by Texas Department of Transportation engineers. Design hyetographs are used in conjunction with unit hydrographs to obtain peak discharge and hydrograph shape for hydraulic design. Storm-depth distributions can be used to assess the probability of a total rainfall depth for a storm. A research project from 2000–2004 has been conducted to (1) determine if existing Natural Resources Conservation Service (NRCS) dimensionless hyetographs are representative of storms in Texas, (2) provide new procedures for dimensionless hyetograph estimation if the NRCS hyetographs are not representative, and (3) provide a procedure to estimate the distribution of storm depth for Texas. This report summarizes the research activities and results of the research project. The report documents several functional models of dimensionless hyetographs and provides curves and tabulated ordinates of empirical (nonfunctional) dimensionless hyetographs for a database of runoff-producing storms in Texas. The dimensionless hyetographs are compared to the NRCS dimensionless hyetographs. The distribution of storm depth is documented for seven values of minimum interevent time through dimensionless frequency curves and tables of mean storm depth for each county in Texas. Conclusions regarding application of the research results are included in the report.

Dimensionless Model of a Thermoelectric Cooling Device Operating at Real Heat Transfer Conditions: Maximum Cooling Capacity Mode

NASA Astrophysics Data System (ADS)

Melnikov, A. A.; Kostishin, V. G.; Alenkov, V. V.

2017-05-01

Real operating conditions of a thermoelectric cooling device are in the presence of thermal resistances between thermoelectric material and a heat medium or cooling object. They limit performance of a device and should be considered when modeling. Here we propose a dimensionless mathematical steady state model, which takes them into account. Analytical equations for dimensionless cooling capacity, voltage, and coefficient of performance (COP) depending on dimensionless current are given. For improved accuracy a device can be modeled with use of numerical or combined analytical-numerical methods. The results of modeling are in acceptable accordance with experimental results. The case of zero temperature difference between hot and cold heat mediums at which the maximum cooling capacity mode appears is considered in detail. Optimal device parameters for maximal cooling capacity, such as fraction of thermal conductance on the cold side y, fraction of current relative to maximal j' are estimated in range of 0.38-0.44 and 0.48-0.95, respectively, for dimensionless conductance K' = 5-100. Also, a method for determination of thermal resistances of a thermoelectric cooling system is proposed.

Dimensionless factors for an alternating-current non-thermal arc plasma

NASA Astrophysics Data System (ADS)

Zhang, Si-Yuan; Li, Xiao-Song; Liu, Jin-Bao; Liu, Jing-Lin; Li, He-Ping; Zhu, Ai-Min

2016-12-01

A gliding arc discharge, as a source of warm plasma combining advantages of both thermal and cold plasmas, would have promising application prospects in the fields of fuel conversion, combustion enhancement, material synthesis, surface modifications, pollution control, etc. In order to gain insight into the features of an alternating-current gliding arc discharge plasma, three dimensionless factors, i.e., the extinction span (ψ), current lag (δ), and heating lag (χ) factors are proposed in this letter based on the measured waveforms of the discharge voltage and current in an AC gliding arc discharge plasma. The influences of the driving frequency of the power supply (f) on these three dimensionless parameters are investigated experimentally with the explanations on the physical meanings of these factors. The experimental results show that a higher value of f would lead to the lower values of ψ and δ, as well as a higher value of χ. These experimental phenomena indicate a lower threshold ignition voltage of the discharges, a lower current-growth inertia of the gliding arcs and a larger relative thermal inertia of the plasmas with increase the driving frequency of the power supply in the operating parameter range studied in this letter.

Identifying a Superfluid Reynolds Number via Dynamical Similarity.

PubMed

Reeves, M T; Billam, T P; Anderson, B P; Bradley, A S

2015-04-17

The Reynolds number provides a characterization of the transition to turbulent flow, with wide application in classical fluid dynamics. Identifying such a parameter in superfluid systems is challenging due to their fundamentally inviscid nature. Performing a systematic study of superfluid cylinder wakes in two dimensions, we observe dynamical similarity of the frequency of vortex shedding by a cylindrical obstacle. The universality of the turbulent wake dynamics is revealed by expressing shedding frequencies in terms of an appropriately defined superfluid Reynolds number, Re(s), that accounts for the breakdown of superfluid flow through quantum vortex shedding. For large obstacles, the dimensionless shedding frequency exhibits a universal form that is well-fitted by a classical empirical relation. In this regime the transition to turbulence occurs at Re(s)≈0.7, irrespective of obstacle width.

Stoichiometric network analysis and associated dimensionless kinetic equations. Application to a model of the Bray-Liebhafsky reaction.

PubMed

Schmitz, Guy; Kolar-Anić, Ljiljana Z; Anić, Slobodan R; Cupić, Zeljko D

2008-12-25

The stoichiometric network analysis (SNA) introduced by B. L. Clarke is applied to a simplified model of the complex oscillating Bray-Liebhafsky reaction under batch conditions, which was not examined by this method earlier. This powerful method for the analysis of steady-states stability is also used to transform the classical differential equations into dimensionless equations. This transformation is easy and leads to a form of the equations combining the advantages of classical dimensionless equations with the advantages of the SNA. The used dimensionless parameters have orders of magnitude given by the experimental information about concentrations and currents. This simplifies greatly the study of the slow manifold and shows which parameters are essential for controlling its shape and consequently have an important influence on the trajectories. The effectiveness of these equations is illustrated on two examples: the study of the bifurcations points and a simple sensitivity analysis, different from the classical one, more based on the chemistry of the studied system.

Unravelling abiotic and biotic controls on the seasonal water balance using data-driven dimensionless diagnostics

NASA Astrophysics Data System (ADS)

Seibert, Simon Paul; Jackisch, Conrad; Ehret, Uwe; Pfister, Laurent; Zehe, Erwin

2017-06-01

The baffling diversity of runoff generation processes, alongside our sketchy understanding of how physiographic characteristics control fundamental hydrological functions of water collection, storage, and release, continue to pose major research challenges in catchment hydrology. Here, we propose innovative data-driven diagnostic signatures for overcoming the prevailing status quo in catchment inter-comparison. More specifically, we present dimensionless double mass curves (dDMC) which allow inference of information on runoff generation and the water balance at the seasonal and annual timescales. By separating the vegetation and winter periods, dDMC furthermore provide information on the role of biotic and abiotic controls in seasonal runoff formation. A key aspect we address in this paper is the derivation of dimensionless expressions of fluxes which ensure the comparability of the signatures in space and time. We achieve this by using the limiting factors of a hydrological process as a scaling reference. We show that different references result in different diagnostics. As such we define two kinds of dDMC which allow us to derive seasonal runoff coefficients and to characterize dimensionless streamflow release as a function of the potential renewal rate of the soil storage. We expect these signatures for storage controlled seasonal runoff formation to remain invariant, as long as the ratios of release over supply and supply over storage capacity develop similarly in different catchments. We test the proposed methods by applying them to an operational data set comprising 22 catchments (12-166 km2) from different environments in southern Germany and hydrometeorological data from 4 hydrological years. The diagnostics are used to compare the sites and to reveal the dominant controls on runoff formation. The key findings are that dDMC are meaningful signatures for catchment runoff formation at the seasonal to annual scale and that the type of scaling strongly

Dimensionless embedding for nonlinear time series analysis

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Aihara, Kazuyuki

2017-09-01

Recently, infinite-dimensional delay coordinates (InDDeCs) have been proposed for predicting high-dimensional dynamics instead of conventional delay coordinates. Although InDDeCs can realize faster computation and more accurate short-term prediction, it is still not well-known whether InDDeCs can be used in other applications of nonlinear time series analysis in which reconstruction is needed for the underlying dynamics from a scalar time series generated from a dynamical system. Here, we give theoretical support for justifying the use of InDDeCs and provide numerical examples to show that InDDeCs can be used for various applications for obtaining the recurrence plots, correlation dimensions, and maximal Lyapunov exponents, as well as testing directional couplings and extracting slow-driving forces. We demonstrate performance of the InDDeCs using the weather data. Thus, InDDeCs can eventually realize "dimensionless embedding" while we enjoy faster and more reliable computations.

Technical characterization of dialysis fluid flow and mass transfer rate in dialyzers with various filtration coefficients using dimensionless correlation equation.

PubMed

Fukuda, Makoto; Yoshimura, Kengo; Namekawa, Koki; Sakai, Kiyotaka

2017-06-01

The objective of the present study is to evaluate the effect of filtration coefficient and internal filtration on dialysis fluid flow and mass transfer coefficient in dialyzers using dimensionless mass transfer correlation equations. Aqueous solution of vitamin B 12 clearances were obtained for REXEED-15L as a low flux dialyzer, and APS-15EA and APS-15UA as high flux dialyzers. All the other design specifications were identical for these dialyzers except for filtration coefficient. The overall mass transfer coefficient was calculated, moreover, the exponents of Reynolds number (Re) and film mass transfer coefficient of the dialysis-side fluid (k D ) for each flow rate were derived from the Wilson plot and dimensionless correlation equation. The exponents of Re were 0.4 for the low flux dialyzer whereas 0.5 for the high flux dialyzers. Dialysis fluid of the low flux dialyzer was close to laminar flow because of its low filtration coefficient. On the other hand, dialysis fluid of the high flux dialyzers was assumed to be orthogonal flow. Higher filtration coefficient was associated with higher k D influenced by mass transfer rate through diffusion and internal filtration. Higher filtration coefficient of dialyzers and internal filtration affect orthogonal flow of dialysis fluid.

Dimensionless size scaling of intrinsic rotation in DIII-D

DOE PAGES

deGrassie, John S.; Solomon, Wayne M.; Rice, J. E.; ...

2016-08-01

A dimensionless empirical scaling for intrinsic toroidal rotation is given; M A ~β Nρ*, where M A is the toroidal velocity divided by the Alfvén velocity, β N the usual normalized β value, and ρ* is the ion gyroradius divided by the minor radius. This scaling describes well experimental data from DIII-D, and also some published data from C-Mod and JET. The velocity used in this scaling is in an outer location in minor radius, outside of the interior core and inside of the large gradient edge region in H-mode conditions. Furthermore, this scaling establishes the basic magnitude of themore » intrinsic toroidal rotation and its relation to the rich variety of rotation profiles that can be realized for intrinsic conditions is discussed.« less

Dimensionless Analysis and Numerical Modeling of Rebalancing Phenomena During Levitation

NASA Astrophysics Data System (ADS)

Gao, Lei; Shi, Zhe; Li, Donghui; McLean, Alexander; Chattopadhyay, Kinnor

2016-06-01

Electromagnetic levitation (EML) has proved to be a powerful tool for research activities in areas pertaining to materials physics and engineering. The customized EML setups in various fields, ranging from solidification to nanomaterial manufacturing, require the designing of stable levitation systems. Since the elevated droplet is opaque, the most effective way to research on EML is mathematical modeling. In the present study, a 3D model was built to investigate the rebalancing phenomenon causing instabilities during droplet melting. A mathematical model modified based on Hooke's law (spring) was proposed to describe the levitation system. This was combined with dimensionless analysis to investigate the generation of levitation forces as it will significantly affect the behavior of the spring model.

Laboratory longitudinal diffusion tests: 1. Dimensionless formulations and validity of simplified solutions

NASA Astrophysics Data System (ADS)

Takeda, M.; Nakajima, H.; Zhang, M.; Hiratsuka, T.

2008-04-01

To obtain reliable diffusion parameters for diffusion testing, multiple experiments should not only be cross-checked but the internal consistency of each experiment should also be verified. In the through- and in-diffusion tests with solution reservoirs, test interpretation of different phases often makes use of simplified analytical solutions. This study explores the feasibility of steady, quasi-steady, equilibrium and transient-state analyses using simplified analytical solutions with respect to (i) valid conditions for each analytical solution, (ii) potential error, and (iii) experimental time. For increased generality, a series of numerical analyses are performed using unified dimensionless parameters and the results are all related to dimensionless reservoir volume (DRV) which includes only the sorptive parameter as an unknown. This means the above factors can be investigated on the basis of the sorption properties of the testing material and/or tracer. The main findings are that steady, quasi-steady and equilibrium-state analyses are applicable when the tracer is not highly sorptive. However, quasi-steady and equilibrium-state analyses become inefficient or impractical compared to steady state analysis when the tracer is non-sorbing and material porosity is significantly low. Systematic and comprehensive reformulation of analytical models enables the comparison of experimental times between different test methods. The applicability and potential error of each test interpretation can also be studied. These can be applied in designing, performing, and interpreting diffusion experiments by deducing DRV from the available information for the target material and tracer, combined with the results of this study.

Vectors for co-expression of an unrestricted number of proteins

PubMed Central

Scheich, Christoph; Kümmel, Daniel; Soumailakakis, Dimitri; Heinemann, Udo; Büssow, Konrad

2007-01-01

A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five ‘pQLink’ vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells. PMID:17311810

Analysis of the effects of atomic mass, jet velocity, and radiative cooling on the dimensionless parameters of counter-propagating, weakly collisional plasma flows

NASA Astrophysics Data System (ADS)

Collins, Gilbert; Valenzuela, Julio; Beg, Farhat

2016-10-01

We have studied the collision of counter-propagating plasma flows using opposing conical wire arrays driven by the 200kA, 150ns rise-time `GenASIS' driver. These plasma flows produced weakly collisional, well-defined bow-shock structures. Varying initial parameters such as the opening angle of the array and the atomic mass of the wires allowed us to modify quantities such as the density contrast between jets, intra-jet mean free path (λmfp, scales with v, atomic mass A, and ionization state Zi-4) , Reynolds number (Re, scales with AZ), and the Peclet number (Pe, scales with Z). We calculate these dimensionless quantities using schlieren imagery, interferometry, and emission data, and determine whether they meet the scaling criteria necessary for the comparison to and subsequent study of astrophysical plasmas. This work was partially supported by the Department of Energy Grant Number DE-SC0014493.

Dimensionless erosion laws for cohesive sediment

USGS Publications Warehouse

Walder, Joseph S.

2016-01-01

A method of achieving a dimensionless collapse of erosion-rate data for cohesive sediments is proposed and shown to work well for data collected in flume-erosion tests on mixtures of sand and mud (silt plus clay sized particles) for a wide range of mud fraction. The data collapse corresponds to a dimensional erosion law of the form E∼(τ−τc)m">E∼(τ−τc)mE∼(τ−τc)m, where E">EE is erosion rate, τ">ττ is shear stress, τc">τcτc is the threshold shear stress for erosion to occur, and m≈7/4">m≈7/4m≈7/4. This result contrasts with the commonly assumed linear erosion law E=kd(τ−τc)">E=kd(τ−τc)E=kd(τ−τc), where kd">kdkd is a measure of how easily sediment is eroded. The data collapse prompts a re-examination of the way that results of the hole-erosion test (HET) and jet-erosion test (JET) are customarily analyzed, and also calls into question the meaningfulness not only of proposed empirical relationships between kd">kdkd and τc">τcτc, but also of the erodibility parameter kd">kdkd itself. Fuller comparison of flume-erosion data with hole-erosion and jet-erosion data will require revised analyses of the HET and JET that drop the assumption m=1">m=1m=1 and, in the case of the JET, certain simplifying assumptions about the mechanics of jet scour.

Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks

PubMed Central

Colon-Perez, Luis M.; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R.; Price, Catherine; Mareci, Thomas H.

2015-01-01

High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime. PMID:26173147

Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks.

PubMed

Colon-Perez, Luis M; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R; Price, Catherine; Mareci, Thomas H

2015-01-01

High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime.

Multi-objective optimization and design for free piston Stirling engines based on the dimensionless power

NASA Astrophysics Data System (ADS)

Mou, Jian; Hong, Guotong

2017-02-01

In this paper, the dimensionless power is used to optimize the free piston Stirling engines (FPSE). The dimensionless power is defined as a ratio of the heat power loss and the output work. The heat power losses include the losses of expansion space, heater, regenerator, cooler and the compression space and every kind of the heat loss calculated by empirical formula. The output work is calculated by the adiabatic model. The results show that 82.66% of the losses come from the expansion space and 54.59% heat losses of expansion space come from the shuttle loss. At different pressure the optimum bore-stroke ratio, heat source temperature, phase angle and the frequency have different values, the optimum phase angles increase with the increase of pressure, but optimum frequencies drop with the increase of pressure. However, no matter what the heat source temperature, initial pressure and frequency are, the optimum ratios of piston stroke and displacer stroke all about 0.8. The three-dimensional diagram is used to analyse Stirling engine. From the three-dimensional diagram the optimum phase angle, frequency and heat source temperature can be acquired at the same time. This study offers some guides for the design and optimization of FPSEs.

Similarity Theory and Dimensionless Numbers in Heat Transfer

ERIC Educational Resources Information Center

Marin, E.; Calderon, A.; Delgado-Vasallo, O.

2009-01-01

We present basic concepts underlying the so-called similarity theory that in our opinion should be explained in basic undergraduate general physics courses when dealing with heat transport problems, in particular with those involving natural or free convection. A simple example is described that can be useful in showing a criterion for neglecting…

Dimensionless Numbers For Morphological, Thermal And Biogeochemical Controls Of Hyporheic Processes

NASA Astrophysics Data System (ADS)

Bellin, Alberto; Marzadri, Alessandra; Tonina, Daniele

2013-04-01

Transport of solutes and heat within the hyporheic zone are interface processes that gained growing attention in the last decade, when several modelling strategies have been proposed, mainly at the local or reach scale. We propose to upscale local hyporheic biogeochemical processes to reach and network scales by means of a Lagrangian modelling framework, which allows to consider the impact of the flow structure on the processes modelled. This analysis shows that geochemical processes can be parametrized through two new Damköhler numbers, DaO, and DaT. DaO = ?up,50-?lim is defined as the ratio between the median hyporheic residence time, ?up,50 and the time of consuming dissolved oxygen to a prescribed threshold concentration, ?lim, below which reductive reactions are activated. It quantifies the biogeochemical status of the hyporheic zone and could be a metric for upscaling local hyporheic biogeochemical processes to reach and river-network scale processes. In addition, ?up,50 is the time scale of hyporheic advection; while ?lim is the representative time scale of biogeochemical reactions and indicates the distance along the streamline, measured as the time needed to travel that distance, that a particle of water travels before the dissolved oxygen concentration declines to [DO]lim, the value at which denitrification is activated. We show that DaO is representative of the redox status and indicates whether the hyporheic zone is a source or a sink of nitrate. Values of DaO larger than 1 indicate prevailing anaerobic conditions, whereas values smaller than 1 prevailing aerobic conditions. Similarly, DaT quantifies the importance of the temperature daily oscillations of the stream water on the hyporheic environment. It is defined as the ratio between ?up,50, and the time limit at which the ratio between the amplitude of the temperature oscillation within the hyporheic zone (evaluated along the streamline) and in the stream water is smaller than e-1. We show that

Study of Nonlinear MHD Tribological Squeeze Film at Generalized Magnetic Reynolds Numbers Using DTM.

PubMed

Rashidi, Mohammad Mehdi; Freidoonimehr, Navid; Momoniat, Ebrahim; Rostami, Behnam

2015-01-01

In the current article, a combination of the differential transform method (DTM) and Padé approximation method are implemented to solve a system of nonlinear differential equations modelling the flow of a Newtonian magnetic lubricant squeeze film with magnetic induction effects incorporated. Solutions for the transformed radial and tangential momentum as well as solutions for the radial and tangential induced magnetic field conservation equations are determined. The DTM-Padé combined method is observed to demonstrate excellent convergence, stability and versatility in simulating the magnetic squeeze film problem. The effects of involved parameters, i.e. squeeze Reynolds number (N1), dimensionless axial magnetic force strength parameter (N2), dimensionless tangential magnetic force strength parameter (N3), and magnetic Reynolds number (Rem) are illustrated graphically and discussed in detail. Applications of the study include automotive magneto-rheological shock absorbers, novel aircraft landing gear systems and biological prosthetics.

Study of Nonlinear MHD Tribological Squeeze Film at Generalized Magnetic Reynolds Numbers Using DTM

PubMed Central

Rashidi, Mohammad Mehdi; Freidoonimehr, Navid; Momoniat, Ebrahim; Rostami, Behnam

2015-01-01

In the current article, a combination of the differential transform method (DTM) and Padé approximation method are implemented to solve a system of nonlinear differential equations modelling the flow of a Newtonian magnetic lubricant squeeze film with magnetic induction effects incorporated. Solutions for the transformed radial and tangential momentum as well as solutions for the radial and tangential induced magnetic field conservation equations are determined. The DTM-Padé combined method is observed to demonstrate excellent convergence, stability and versatility in simulating the magnetic squeeze film problem. The effects of involved parameters, i.e. squeeze Reynolds number (N 1), dimensionless axial magnetic force strength parameter (N 2), dimensionless tangential magnetic force strength parameter (N 3), and magnetic Reynolds number (Re m) are illustrated graphically and discussed in detail. Applications of the study include automotive magneto-rheological shock absorbers, novel aircraft landing gear systems and biological prosthetics. PMID:26267247

Relativistic theory of tidal Love numbers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Binnington, Taylor; Poisson, Eric

In Newtonian gravitational theory, a tidal Love number relates the mass multipole moment created by tidal forces on a spherical body to the applied tidal field. The Love number is dimensionless, and it encodes information about the body's internal structure. We present a relativistic theory of Love numbers, which applies to compact bodies with strong internal gravities; the theory extends and completes a recent work by Flanagan and Hinderer, which revealed that the tidal Love number of a neutron star can be measured by Earth-based gravitational-wave detectors. We consider a spherical body deformed by an external tidal field, and providemore » precise and meaningful definitions for electric-type and magnetic-type Love numbers; and these are computed for polytropic equations of state. The theory applies to black holes as well, and we find that the relativistic Love numbers of a nonrotating black hole are all zero.« less

Patients prefer pictures to numbers to express cardiovascular benefit from treatment.

PubMed

Goodyear-Smith, Felicity; Arroll, Bruce; Chan, Lydia; Jackson, Rod; Wells, Sue; Kenealy, Timothy

2008-01-01

This study aimed to determine which methods of expressing a preventive medication's benefit encourage patients with known cardiovascular disease to decide to take the medication and which methods patients prefer. We identified patients in Auckland, New Zealand, family practices located in areas of differing socioeconomic status who had preexisting heart disease (myocardial infarction, angina, or both) and were taking statins. The patients were interviewed about their preference for methods of expressing the benefit of a hypothetical medication. Benefits were expressed numerically (relative risk, absolute risk, number needed to treat, odds ratio, natural frequency) and graphically. Statistical testing was adjusted for practice. We interviewed 100 eligible patients, representing a 53% response rate. No matter how the risk was expressed, the majority of patients indicated they would be encouraged to take the medication. Two-thirds (68) of the patients preferred 1 method of expressing benefit over others. Of this group, 57% preferred the information presented graphically. This value was significantly greater (P <.001) than the 19% who chose the next most preferred option, relative risk. Few patients preferred absolute risk (13%) or natural frequencies (9%). Only a single patient (1%) preferred the odds ratio. None preferred number needed to treat. Ninety percent of patients responding to a question about framing preferred positive framing (description of the benefit of treatment) over negative framing (description of the harm of not being treated). Although number needed to treat is a useful tool for communicating risk and benefit to clinicians, this format was the least likely to encourage patients to take medication. As graphical representation of benefit was the method patients preferred most, consideration should be given to developing visual aids to support shared clinical decision making.

From DNA Copy Number to Gene Expression: Local aberrations, Trisomies and Monosomies

NASA Astrophysics Data System (ADS)

Shay, Tal

The goal of my PhD research was to study the effect of DNA copy number changes on gene expression. DNA copy number aberrations may be local, encompassing several genes, or on the level of an entire chromosome, such as trisomy and monosomy. The main dataset I studied was of Glioblastoma, obtained in the framework of a collaboration, but I worked also with public datasets of cancer and Down's Syndrome. The molecular basis of expression changes in Glioblastoma. Glioblastoma is the most common and aggressive type of primary brain tumors in adults. In collaboration with Prof. Hegi (CHUV, Switzerland), we analyzed a rich Glioblastoma dataset including clinical information, DNA copy number (array CGH) and expression profiles. We explored the correlation between DNA copy number and gene expression at the level of chromosomal arms and local genomic aberrations. We detected known amplification and over expression of oncogenes, as well as deletion and down-regulation of tumor suppressor genes. We exploited that information to map alterations of pathways that are known to be disrupted in Glioblastoma, and tried to characterize samples that have no known alteration in any of the studied pathways. Identifying local DNA aberrations of biological significance. Many types of tumors exhibit chromosomal losses or gains and local amplifications and deletions. A region that is aberrant in many tumors, or whose copy number change is stronger, is more likely to be clinically relevant, and not just a by-product of genetic instability. We developed a novel method that defines and prioritizes aberrations by formalizing these intuitions. The method scores each aberration by the fraction of patients harboring it, its length and its amplitude, and assesses the significance of the score by comparing it to a null distribution obtained by permutations. This approach detects genetic locations that are significantly aberrant, generating a 'genomic aberration profile' for each sample. The 'genomic

THE DIMENSIONLESS AGE OF THE UNIVERSE: A RIDDLE FOR OUR TIME

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avelino, Arturo; Kirshner, Robert P., E-mail: aavelino@cfa.harvard.edu

We present the interesting coincidence of cosmology and astrophysics that points toward a dimensionless age of the Universe H {sub 0} t {sub 0} that is close to one. Despite cosmic deceleration for 9 Gyr and acceleration since then, we find H {sub 0} t {sub 0} = 0.96 ± 0.01 for the ΛCDM model that fits SN Ia data from Pan-STARRS, CMB power spectra, and baryon acoustic oscillations. Similarly, astrophysical measures of stellar ages and the Hubble constant derived from redshifts and distances point to H {sub 0} t ∼ 1.0 ± 0.1. The wide range of possible valuesmore » for H {sub 0} t {sub 0} realized during cosmic evolution means that we live at what appears to be a special time. This “synchronicity problem” is not precisely the same as the usual coincidence problem , because there are combinations of Ω{sub M} and Ω{sub Λ} for which the usual coincidence problem holds but for which H {sub 0} t {sub 0} is not close to 1.« less

On the number of light rings in curved spacetimes of ultra-compact objects

NASA Astrophysics Data System (ADS)

Hod, Shahar

2018-01-01

In a very interesting paper, Cunha, Berti, and Herdeiro have recently claimed that ultra-compact objects, self-gravitating horizonless solutions of the Einstein field equations which have a light ring, must possess at least two (and, in general, an even number of) light rings, of which the inner one is stable. In the present compact paper we explicitly prove that, while this intriguing theorem is generally true, there is an important exception in the presence of degenerate light rings which, in the spherically symmetric static case, are characterized by the simple dimensionless relation 8 πrγ2 (ρ +pT) = 1 [here rγ is the radius of the light ring and { ρ ,pT } are respectively the energy density and tangential pressure of the matter fields]. Ultra-compact objects which belong to this unique family can have an odd number of light rings. As a concrete example, we show that spherically symmetric constant density stars with dimensionless compactness M / R = 1 / 3 possess only one light ring which, interestingly, is shown to be unstable.

Rayleigh- and Prandtl-number dependence of the large-scale flow-structure in weakly-rotating turbulent thermal convection

NASA Astrophysics Data System (ADS)

Weiss, Stephan; Wei, Ping; Ahlers, Guenter

2015-11-01

Turbulent thermal convection under rotation shows a remarkable variety of different flow states. The Nusselt number (Nu) at slow rotation rates (expressed as the dimensionless inverse Rossby number 1/Ro), for example, is not a monotonic function of 1/Ro. Different 1/Ro-ranges can be observed with different slopes ∂Nu / ∂ (1 / Ro) . Some of these ranges are connected by sharp transitions where ∂Nu / ∂ (1 / Ro) changes discontinuously. We investigate different regimes in cylindrical samples of aspect ratio Γ = 1 by measuring temperatures at the sidewall of the sample for various Prandtl numbers in the range 3 < Pr < 35 and Rayleigh numbers in the range of 108 < Ra < 4 ×1011 . From these measurements we deduce changes of the flow structure. We learn about the stability and dynamics of the large-scale circulation (LSC), as well as about its breakdown and the onset of vortex formation close to the top and bottom plate. We shall examine correlations between these measurements and changes in the heat transport. This work was supported by NSF grant DRM11-58514. SW acknowledges support by the Deutsche Forschungsgemeinschaft.

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.

PubMed

Salari, Keyan; Tibshirani, Robert; Pollack, Jonathan R

2010-02-01

DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes. DR-Integrator is freely available for non-commercial use from the Pollack Lab at http://pollacklab.stanford.edu/ and can be downloaded as a plug-in application to Microsoft Excel and as a package for the R statistical computing environment. The R package is available under the name 'DRI' at http://cran.r-project.org/. An example analysis using DR-Integrator is included as supplemental material. Supplementary data are available at Bioinformatics online.

Engineered promoters enable constant gene expression at any copy number in bacteria.

PubMed

Segall-Shapiro, Thomas H; Sontag, Eduardo D; Voigt, Christopher A

2018-04-01

The internal environment of growing cells is variable and dynamic, making it difficult to introduce reliable parts, such as promoters, for genetic engineering. Here, we applied control-theoretic ideas to design promoters that maintained constant levels of expression at any copy number. Theory predicts that independence to copy number can be achieved by using an incoherent feedforward loop (iFFL) if the negative regulation is perfectly non-cooperative. We engineered iFFLs into Escherichia coli promoters using transcription-activator-like effectors (TALEs). These promoters had near-identical expression in different genome locations and plasmids, even when their copy number was perturbed by genomic mutations or changes in growth medium composition. We applied the stabilized promoters to show that a three-gene metabolic pathway to produce deoxychromoviridans could retain function without re-tuning when the stabilized-promoter-driven genes were moved from a plasmid into the genome.

Effects of End Conditions of Cross-Ply Laminated Composite Beams on Their Dimensionless Natural Frequencies

NASA Astrophysics Data System (ADS)

Algarray, A. F. A.; Jun, H.; Mahdi, I.-E. M.

2017-11-01

The effects of the end conditions of cross-ply laminated composite beams on their dimensionless natural frequencies of free vibration is investigated. The problem is analyzed and solved by using the energy approach, which is formulated by a finite element model. Various end conditions of beams are used. Each beam has either movable ends or immovable ends. Numerical results are verified by comparisons with other relevant works. It is found that more constrained beams have higher values of natural frequencies of transverse vibration. The values of the natural frequencies of longitudinal modes are found to be the same for all beams with movable ends because they are generated by longitudinal movements only.

A New Dimensionless Number for Redox Conditions within the Hyporheic Zone: Morphological and Biogeochemical Controls

NASA Astrophysics Data System (ADS)

Marzadri, A.; Tonina, D.; Bellin, A.

2012-12-01

We introduce a new Damköhler number, Da, to quantify the biogeochemical status of the hyporheic zone and to upscale local hyporheic processes to reach scale. Da is defined as the ratio between the median hyporheic residence time, τup,50, which is a representative time scale of the hyporheic flow, and a representative time scale of biogeochemical reactions, which we define as the time τlim needed to consume dissolved oxygen to a prescribed threshold concentration below which reducing reactions are activated: Da = τup,50/τlim. This approach accounts for streambed topography and surface hydraulics via the hyporheic residence time and biogeochemical reaction via the time limit τlim. Da can readily evaluate the redox status of the hyporheic zone. Values of Da larger than 1 indicate prevailing anaerobic conditions, whereas values smaller than 1 prevailing aerobic conditions. This new Damköhler number can quantify the efficiency of hyporheic zone in transforming dissolved inorganic nitrogen species such as ammonium and nitrate, whose transformation depends on the redox condition of the hyporheic zone. We define a particular value of Da, Das, that indicates when the hyporheic zone is a source or a sink of nitrate. This index depends only on the relative abundance of ammonium and nitrate. The approach can be applied to any hyporheic zone of which the median hyporheic residence time is known. Application to streams with pool-riffle morphology shows that Da increases passing from small to large streams implying that the fraction of the hyporheic zone in anaerobic conditions increases with stream size.

Dimensionless parameterization of lidar for laser remote sensing of the atmosphere and its application to systems with SiPM and PMT detectors.

PubMed

Agishev, Ravil; Comerón, Adolfo; Rodriguez, Alejandro; Sicard, Michaël

2014-05-20

In this paper, we show a renewed approach to the generalized methodology for atmospheric lidar assessment, which uses the dimensionless parameterization as a core component. It is based on a series of our previous works where the problem of universal parameterization over many lidar technologies were described and analyzed from different points of view. The modernized dimensionless parameterization concept applied to relatively new silicon photomultiplier detectors (SiPMs) and traditional photomultiplier (PMT) detectors for remote-sensing instruments allowed predicting the lidar receiver performance with sky background available. The renewed approach can be widely used to evaluate a broad range of lidar system capabilities for a variety of lidar remote-sensing applications as well as to serve as a basis for selection of appropriate lidar system parameters for a specific application. Such a modernized methodology provides a generalized, uniform, and objective approach for evaluation of a broad range of lidar types and systems (aerosol, Raman, DIAL) operating on different targets (backscatter or topographic) and under intense sky background conditions. It can be used within the lidar community to compare different lidar instruments.

Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes

PubMed Central

Tokar, Tomas; Pastrello, Chiara; Ramnarine, Varune R.; Zhu, Chang-Qi; Craddock, Kenneth J.; Pikor, Larrisa A.; Vucic, Emily A.; Vary, Simon; Shepherd, Frances A.; Tsao, Ming-Sound; Lam, Wan L.; Jurisica, Igor

2018-01-01

In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status. PMID:29507679

Mode tuning of a simplified string instrument using time-dimensionless state-derivative control

NASA Astrophysics Data System (ADS)

Benacchio, Simon; Chomette, Baptiste; Mamou-Mani, Adrien; Finel, Victor

2015-01-01

In recent years, there has been a growing interest in smart structures, particularly in the field of musical acoustics. Control methods, initially developed to reduce vibration and damage, can be a good way to shift modal parameters of a structure in order to modify its dynamic response. This study focuses on smart musical instruments and aims to modify their radiated sound. This is achieved by controlling the modal parameters of the soundboard of a simplified string instrument. A method combining a pole placement algorithm and a time-dimensionless state-derivative control is used and quickly compared to a usual state control method. Then the effect of the mode tuning on the coupling between the string and the soundboard is experimentally studied. Controlling two vibration modes of the soundboard, its acoustic response and the damping of the third partial of the sound are modified. Finally these effects are listened in the radiated sound.

[Gene copy number, mRNA transcription and protein expression of PD-1 gene in primary hepatocarcinoma patients].

PubMed

Fan, Hui-Min; Wu, Ling-Jie; Hu, Feng-Yu; Yang, Zhan

2012-08-01

To study the gene copy number, mRNA transcription and protien expression of programmed cell death 1 (PD-1) gene in primary hepatocellular carcinoma (PHC) patients and normal control individuals (NC) who are anti-HBs positive, and to investigate the variations in PD-1 gene copy numbers and its relationship with PHC. Real-time PCR was adopted to detect the PD-1 gene copy numbers and their mRNA expressions in peripheral blood mononuclear cells (PBMCs) from 24 samples of PHC patients and 26 of NC. Protein expression level of PD-1 on CD8+ T was analyzed by flow cytometry. In terms of number of PD-1 gene copy numbers, the percentage of cases of haploid (single) was 34.62% and 4.17% in PHC group and control group respectively while the percentage of cases of diploid (double) was 61.54% and 95.83% respectively. The difference between the two was statistically significant (chi2 = 7.639, P = 0.006). The rate of cases with double PD-1 gene copy numbers was found to be higher in patients with PHC than in control group. It was also found that the average expression of PD-1 mRNA was 2.35E-03 in control group and 1.23E-03 in PHC group. The expression level was significant lower in PHC group than that in control group when compared by using Mann-whitey technic (U = 153, P = 0.009). Furthermore, the frequency of PD-1 protein expression on CD8+ T cells was 3.72 +/- 0.32 in control group and 16.13 +/- 1.68 in PHC group. The level of PD-1 mRNA expression was higher in PHC and significant differences was shown between two groups (t = -7.073, P = 0.000). Our study suggests that the variation in PD-1 gene copy number may trigger primary hepatocellular carcinoma to HBV carriers. The relationship between the variation of PD-1 gene copy numbers and its association with primary hepatocellular carcinoma is worth further focus.

The number of striatal cholinergic interneurons expressing calretinin is increased in parkinsonian monkeys.

PubMed

Petryszyn, Sarah; Di Paolo, Thérèse; Parent, André; Parent, Martin

2016-11-01

The most abundant interneurons in the primate striatum are those expressing the calcium-binding protein calretinin (CR). The present immunohistochemical study provides detailed assessments of their morphological traits, number, and topographical distribution in normal monkeys (Macaca fascicularis) and in monkeys rendered parkinsonian (PD) by MPTP intoxication. In primates, the CR+ striatal interneurons comprise small (8-12μm), medium (12-20μm) and large-sized (20-45μm) neurons, each with distinctive morphologies. The small CR+ neurons were 2-3 times more abundant than the medium-sized CR+ neurons, which were 20-40 times more numerous than the large CR+ neurons. In normal and PD monkeys, the density of small and medium-sized CR+ neurons was twice as high in the caudate nucleus than in the putamen, whereas the inverse occurred for the large CR+ neurons. Double immunostaining experiments revealed that only the large-sized CR+ neurons expressed choline acetyltransferase (ChAT). The number of large CR+ neurons was found to increase markedly (4-12 times) along the entire anteroposterior extent of both the caudate nucleus and putamen of PD monkeys compared to controls. Comparison of the number of large CR-/ChAT+ and CR+/ChAT+ neurons together with experiments involving the use of bromo-deoxyuridine (BrdU) as a marker of newly generated cells showed that it is the expression of CR by the large ChAT+ striatal interneurons, and not their absolute number, that is increased in the dopamine-depleted striatum. These findings reveal the modulatory role of dopamine in the phenotypic expression of the large cholinergic striatal neurons, which are known to play a crucial role in PD pathophysiology. Copyright © 2016 Elsevier Inc. All rights reserved.

Flying and swimming animals cruise at a Strouhal number tuned for high power efficiency.

PubMed

Taylor, Graham K; Nudds, Robert L; Thomas, Adrian L R

2003-10-16

Dimensionless numbers are important in biomechanics because their constancy can imply dynamic similarity between systems, despite possible differences in medium or scale. A dimensionless parameter that describes the tail or wing kinematics of swimming and flying animals is the Strouhal number, St = fA/U, which divides stroke frequency (f) and amplitude (A) by forward speed (U). St is known to govern a well-defined series of vortex growth and shedding regimes for airfoils undergoing pitching and heaving motions. Propulsive efficiency is high over a narrow range of St and usually peaks within the interval 0.2 < St < 0.4 (refs 3-8). Because natural selection is likely to tune animals for high propulsive efficiency, we expect it to constrain the range of St that animals use. This seems to be true for dolphins, sharks and bony fish, which swim at 0.2 < St < 0.4. Here we show that birds, bats and insects also converge on the same narrow range of St, but only when cruising. Tuning cruise kinematics to optimize St therefore seems to be a general principle of oscillatory lift-based propulsion.

Explicit analytical expression for the condition number of polynomials in power form

NASA Astrophysics Data System (ADS)

Rack, Heinz-Joachim

2017-07-01

In his influential papers [1-3] W. Gautschi has defined and reshaped the condition number κ∞ of polynomials Pn of degree ≤ n which are represented in power form on a zero-symmetric interval [-ω, ω]. Basically, κ∞ is expressed as the product of two operator norms: an explicit factor times an implicit one (the l∞-norm of the coefficient vector of the n-th Chebyshev polynomial of the first kind relative to [-ω, ω]). We provide a new proof, economize the second factor and express it by an explicit analytical formula.

Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data.

PubMed

Yoshida, Tsuyoshi; Kobayashi, Takumi; Itoda, Masaya; Muto, Taika; Miyaguchi, Ken; Mogushi, Kaoru; Shoji, Satoshi; Shimokawa, Kazuro; Iida, Satoru; Uetake, Hiroyuki; Ishikawa, Toshiaki; Sugihara, Kenichi; Mizushima, Hiroshi; Tanaka, Hiroshi

2010-07-29

Colorectal cancer (CRC) is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC) and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an "omics" study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene expression analysis, together with the clinical information

[High-level expression of heterologous protein based on increased copy number in Saccharomyces cerevisiae].

PubMed

Zhang, Xinjie; He, Peng; Tao, Yong; Yang, Yi

2013-11-04

High-level expression system of heterologous protein mediated by internal ribosome entry site (IRES) in Saccharomyces cerevisiae was constructed, which could be used for other applications of S. cerevisiae in metabolic engineering. We constructed co-expression cassette (promoter-mCherry-TIF4631 IRES-URA3) containing promoters Pilv5, Padh2 and Ptdh3 and recombined the co-expression cassette into the genome of W303-1B-A. The URA3+ transformants were selected. By comparing the difference in the mean florescence value of mCherry in transformants, the effect of three promoters was detected in the co-expression cassette. The copy numbers of the interested genes in the genome were determined by Real-Time PCR. We analyzed genetic stability by continuous subculturing transformants in the absence of selection pressure. To verify the application of co-expression cassette, the ORF of mCherry was replaced by beta-galactosidase (LACZ) and xylose reductase (XYL1). The enzyme activities and production of beta-galactosidase and xylose reductase were detected. mCherry has been expressed in the highest-level in transformants with co-expression cassette containing Pilv5 promoter. The highest copy number of DNA fragment integrating in the genome was 47 in transformants containing Pilv5. The engineering strains showed good genetic stability. Xylose reductase was successfully expressed in the co-expression cassette containing Pilv5 promoter and TIF4631 IRES. The highest enzyme activity was 0. 209 U/mg crude protein in the transformants WIX-10. Beta-galactosidase was also expressed successfully. The transformants that had the highest enzyme activity was WIL-1 and the enzyme activity was 12.58 U/mg crude protein. The system mediated by Pilv5 promoter and TIF4631 IRES could express heterologous protein efficiently in S. cerevisiae. This study offered a new strategy for expression of heterologous protein in S. cerevisiae and provided sufficient experimental evidence for metabolic engineering

Common Spatial Organization of Number and Emotional Expression: A Mental Magnitude Line

ERIC Educational Resources Information Center

Holmes, Kevin J.; Lourenco, Stella F.

2011-01-01

Converging behavioral and neural evidence suggests that numerical representations are mentally organized in left-to-right orientation. Here we show that this format of spatial organization extends to emotional expression. In Experiment 1, right-side responses became increasingly faster as number (represented by Arabic numerals) or happiness…

Threshold and flavor effects in the renormalization group equations of the MSSM: Dimensionless couplings

NASA Astrophysics Data System (ADS)

Box, Andrew D.; Tata, Xerxes

2008-03-01

In a theory with broken supersymmetry, gaugino couplings renormalize differently from gauge couplings, as do higgsino couplings from Higgs boson couplings. As a result, we expect the gauge (Higgs boson) couplings and the corresponding gaugino (higgsino) couplings to evolve to different values under renormalization group evolution. We reexamine the renormalization group equations (RGEs) for these couplings in the minimal supersymmetric standard model (MSSM). To include threshold effects, we calculate the β functions using a sequence of (nonsupersymmetric) effective theories with heavy particles decoupled at the scale of their mass. We find that the difference between the SM couplings and their SUSY cousins that is ignored in the literature may be larger than two-loop effects which are included, and further that renormalization group evolution induces a nontrivial flavor structure in gaugino interactions. We present here the coupled set of RGEs for these dimensionless gauge and Yukawa-type couplings. The RGEs for the dimensionful soft-supersymmetry-breaking parameters of the MSSM will be presented in a companion paper.

iGC-an integrated analysis package of gene expression and copy number alteration.

PubMed

Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

2017-01-14

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

Hydrologic classification of rivers based on cluster analysis of dimensionless hydrologic signatures: Applications for environmental instream flows

NASA Astrophysics Data System (ADS)

Praskievicz, S. J.; Luo, C.

2017-12-01

Classification of rivers is useful for a variety of purposes, such as generating and testing hypotheses about watershed controls on hydrology, predicting hydrologic variables for ungaged rivers, and setting goals for river management. In this research, we present a bottom-up (based on machine learning) river classification designed to investigate the underlying physical processes governing rivers' hydrologic regimes. The classification was developed for the entire state of Alabama, based on 248 United States Geological Survey (USGS) stream gages that met criteria for length and completeness of records. Five dimensionless hydrologic signatures were derived for each gage: slope of the flow duration curve (indicator of flow variability), baseflow index (ratio of baseflow to average streamflow), rising limb density (number of rising limbs per unit time), runoff ratio (ratio of long-term average streamflow to long-term average precipitation), and streamflow elasticity (sensitivity of streamflow to precipitation). We used a Bayesian clustering algorithm to classify the gages, based on the five hydrologic signatures, into distinct hydrologic regimes. We then used classification and regression trees (CART) to predict each gaged river's membership in different hydrologic regimes based on climatic and watershed variables. Using existing geospatial data, we applied the CART analysis to classify ungaged streams in Alabama, with the National Hydrography Dataset Plus (NHDPlus) catchment (average area 3 km2) as the unit of classification. The results of the classification can be used for meeting management and conservation objectives in Alabama, such as developing statewide standards for environmental instream flows. Such hydrologic classification approaches are promising for contributing to process-based understanding of river systems.

Flow and thermal characteristics of high Reynolds number (2800-17,000) dye cell: simulation and experiment.

PubMed

Mishra, G K; Kumar, Abhay; Prakash, O; Biswal, R; Dixit, S K; Nakhe, S V

2015-04-10

This paper presents computational and experimental studies on wavelength/frequency fluctuation characteristics of a high pulse repetition rate (18 kHz) dye laser pumped by a frequency-doubled Nd:YAG laser (532 nm). The temperature gradient in the dye solution is found to be responsible for wavelength fluctuations of the dye laser at low flow rates (2800number (ReT) and the range of eddy sizes present in the turbulent flow are found to be responsible for the fluctuations at high flow rates (8400dimensionless parameter, dimensionless eddy size (l(+)), has been defined to correlate the range of eddy sizes with the experimentally observed wavelength fluctuations. It was found that fluctuations can be controlled by keeping ReT≈10 and lmax(+)≈1. The simulated result explains the experimental observation and provides a basis for optimizing the dye solution flow rate for high PRR pumping.

Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis.

PubMed

Chapman, Mark A; Mukund, Kavitha; Subramaniam, Shankar; Brenner, David; Lieber, Richard L

2017-02-01

Tissue extracellular matrix (ECM) provides structural support and creates unique environments for resident cells (Bateman JF, Boot-Handford RP, Lamandé SR. Nat Rev Genet 10: 173-183, 2009; Kjaer M. Physiol Rev 84: 649-98, 2004). However, the identities of cells responsible for creating specific ECM components have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain the ECM in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I-expressing cells in all three cell populations increases proportionally in fibrotic muscle, indicating that all cell types participate in the fibrosis process. Furthermore, while some profibrotic ECM and ECM-associated genes are significantly upregulated in fibrotic muscle, the fibrillar collagen gene expression profile is not qualitatively altered. This suggests that muscle fibrosis in this model results from an increased number of collagen I-expressing cells and not the initiation of a specific fibrotic collagen gene expression program. Finally, in fibrotic muscle, we show that these collagen I-expressing cell populations differentially express distinct ECM proteins-fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins, and skeletal muscle progenitor cells differentially express genes important for the satellite cell. Copyright © 2017 the American Physiological Society.

Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis

PubMed Central

Chapman, Mark A.; Mukund, Kavitha; Subramaniam, Shankar; Brenner, David

2017-01-01

Tissue extracellular matrix (ECM) provides structural support and creates unique environments for resident cells (Bateman JF, Boot-Handford RP, Lamandé SR. Nat Rev Genet 10: 173–183, 2009; Kjaer M. Physiol Rev 84: 649–98, 2004). However, the identities of cells responsible for creating specific ECM components have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain the ECM in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I-expressing cells in all three cell populations increases proportionally in fibrotic muscle, indicating that all cell types participate in the fibrosis process. Furthermore, while some profibrotic ECM and ECM-associated genes are significantly upregulated in fibrotic muscle, the fibrillar collagen gene expression profile is not qualitatively altered. This suggests that muscle fibrosis in this model results from an increased number of collagen I-expressing cells and not the initiation of a specific fibrotic collagen gene expression program. Finally, in fibrotic muscle, we show that these collagen I-expressing cell populations differentially express distinct ECM proteins—fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins, and skeletal muscle progenitor cells differentially express genes important for the satellite cell. PMID:27881411

Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma

PubMed Central

Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

2017-01-01

Objective This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Methods Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Results Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification (P=0.009) or deletion (P=0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly (P=1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Conclusion Chromosomal CNVs may contribute to their transcript expression in cervical cancer. PMID:29312578

Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma.

PubMed

Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

2017-12-12

This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification ( P =0.009) or deletion ( P =0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly ( P =1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Chromosomal CNVs may contribute to their transcript expression in cervical cancer.

The number of preproghrelin mRNA expressing cells is increased in mice with activity-based anorexia.

PubMed

François, Marie; Barde, Swapnali; Achamrah, Najate; Breton, Jonathan; do Rego, Jean-Claude; Coëffier, Moïse; Hökfelt, Tomas; Déchelotte, Pierre; Fetissov, Sergueï O

2015-06-01

Plasma levels of ghrelin, an orexigenic peptide, are increased during conditions of chronic starvation, such as in patients with anorexia nervosa. However, it is not known whether such increase can be related to the number of preproghrelin mRNA-expressing cells in the stomach, and if chronic starvation may activate a tentative central ghrelin production. In this work, in situ hybridization technique was used to analyze the presence and number of preproghrelin mRNA-expressing cells in the stomach and the hypothalamus of mice with activity-based anorexia (ABA) induced by the combination of running wheel activity with progressive, during 10 days, feeding-time restriction (FTR) and compared with sedentary FTR, ABA pair-fed (PF) and ad libitum-fed control mice. All food-restricted mice lost more than 20% of body weight. Body weight loss was similar in ABA and PF mice, but it was more pronounced than in FTR mice. Food intake was also lower in ABA than in FTR mice. Preproghrelin mRNA-expressing cells in the stomach were increased proportionally to the body weight loss in all food-restricted groups with the highest number in ABA mice. No preproghrelin mRNA-producing cells were detectable in the hypothalamus of either control or food-restricted mice. Thus, the increased number of gastric preproghrelin mRNA-producing cells during chronic starvation proportionally to the body weight loss and reduced food intake may underlie increased plasma ghrelin. Hyperactivity-induced anorexia appears to further increase the number of preproghrelin mRNA-producing cells in the stomach. No evidence was found for ghrelin expression in the hypothalamus, not even in any of the present experimental models. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization of self-acting step thrust bearings for load capacity and stiffness.

NASA Technical Reports Server (NTRS)

Hamrock, B. J.

1972-01-01

Linearized analysis of a finite-width rectangular step thrust bearing. Dimensionless load capacity and stiffness are expressed in terms of a Fourier cosine series. The dimensionless load capacity and stiffness were found to be a function of the dimensionless bearing number, the pad length-to-width ratio, the film thickness ratio, the step location parameter, and the feed groove parameter. The equations obtained in the analysis were verified. The assumptions imposed were substantiated by comparing the results with an existing exact solution for the infinite width bearing. A digital computer program was developed which determines optimal bearing configuration for maximum load capacity or stiffness. Simple design curves are presented. Results are shown for both compressible and incompressible lubrication. Through a parameter transformation the results are directly usable in designing optimal step sector thrust bearings.

Tightly regulated, high-level expression from controlled copy number vectors based on the replicon of temperate phage N15.

PubMed

Mardanov, Andrey V; Strakhova, Taisia S; Smagin, Vladimir A; Ravin, Nikolai V

2007-06-15

A new Escherichia coli host/vector system has been developed to allow a dual regulation of both the plasmid copy number and gene expression. The new pN15E vectors are low copy number plasmids based on the replicon of temperate phage N15, comprising the repA replicase gene and cB repressor gene, controlling the plasmid copy number. Regulation of pN15E copy number is achieved through arabinose-inducible expression of phage N15 antirepressor protein, AntA, whose gene was integrated into the chromosome of the host strain under control of the PBAD promoter. The host strain also carried phage N15 partition operon, sop, allowing stable inheritance of pN15E vectors in the absence of selection pressure. In the first vector, pN15E4, the same PBAD promoter controls expression of a cloned gene. The second vector, pN15E6, carries the phage T5 promoter with a double lac operator repression module thus allowing independent regulation of promoter activity and copy number. Using the lacZ gene to monitor expression in these vectors, we show that the ratio of induction/repression can be about 7600-fold for pN15E4 and more than 15,000-fold for pN15E6. The low copy number of these vectors ensures very low basal level of expression allowing cloning genes encoding toxic products that was demonstrated by the stable maintenance of a gene encoding a restriction endonuclease in pN15E4. The tight control of transcription and the potential to regulate gene activities quantitatively over wide ranges will open up new approaches in the study of gene function in vivo and controlled expression of heterologous genes.

Correlation of Water Frost Porosity in Laminar Flow over Flat Surfaces

NASA Technical Reports Server (NTRS)

Kandula, Max

2011-01-01

A dimensionless correlation has been proposed for water frost porosity expressing its dependence on frost surface temperature and Reynolds number for laminar forced flow over a flat surface. The correlation is presented in terms of a dimensionless frost surface temperature scaled with the cold plate temperature, and the freezing temperature. The flow Reynolds number is scaled with reference to the critical Reynolds number for laminar-turbulent transition. The proposed correlation agrees satisfactorily with the simultaneous measurements of frost density and frost surface temperature covering a range of plate temperature, ambient air velocity, humidity, and temperature. It is revealed that the frost porosity depends primarily on the frost surface and the plate temperatures and the flow Reynolds number, and is only weakly dependent on the relative humidity. The results also point out the general character of frost porosity displaying a decrease with an increase in flow Reynolds number.

Integrative analysis of copy number alteration and gene expression profiling in ovarian clear cell adenocarcinoma.

PubMed

Sung, Chang Ohk; Choi, Chel Hun; Ko, Young-Hyeh; Ju, Hyunjeong; Choi, Yoon-La; Kim, Nyunsu; Kang, So Young; Ha, Sang Yun; Choi, Kyusam; Bae, Duk-Soo; Lee, Jeong-Won; Kim, Tae-Joong; Song, Sang Yong; Kim, Byoung-Gie

2013-05-01

Ovarian clear cell adenocarcinoma (Ov-CCA) is a distinctive subtype of ovarian epithelial carcinoma. In this study, we performed array comparative genomic hybridization (aCGH) and paired gene expression microarray of 19 fresh-frozen samples and conducted integrative analysis. For the copy number alterations, significantly amplified regions (false discovery rate [FDR] q <0.05) were 1q21.3 and 8q24.3, and significantly deleted regions were 3p21.31, 4q12, 5q13.2, 5q23.2, 5q31.1, 7p22.1, 7q11.23, 8p12, 9p22.1, 11p15.1, 12p13.31, 15q11.2, 15q21.2, 18p11.31, and 22q11.21 using the Genomic Identification of Significant Targets in Cancer (GISTIC) analysis. Integrative analysis revealed 94 genes demonstrating frequent copy number alterations (>25% of samples) that correlated with gene expression (FDR <0.05). These genes were mainly located on 8p11.21, 8p21.2-p21.3, 8q22.1, 8q24.3, 17q23.2-q23.3, 19p13.3, and 19p13.11. Among the regions, 8q24.3 was found to contain the most genes (30 of 94 genes) including PTK2. The 8q24.3 region was indicated as the most significant region, as supported by copy number, GISTIC, and integrative analysis. Pathway analysis using differentially expressed genes on 8q24.3 revealed several major nodes, including PTK2. In conclusion, we identified a set of 94 candidate genes with frequent copy number alterations that correlated with gene expression. Specific chromosomal alterations, such as the 8q24.3 gain containing PTK2, could be a therapeutic target in a subset of Ov-CCAs. Copyright © 2013. Published by Elsevier Inc.

Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies

PubMed Central

2010-01-01

Background Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. Results Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. Conclusions Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data. PMID:21062443

Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies.

PubMed

Chen, Bo; Chen, Minhua; Paisley, John; Zaas, Aimee; Woods, Christopher; Ginsburg, Geoffrey S; Hero, Alfred; Lucas, Joseph; Dunson, David; Carin, Lawrence

2010-11-09

Nonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the number of appropriate factors from the observed data. We consider such techniques for sparse factor analysis, with application to gene-expression data from three virus challenge studies. Particular attention is placed on employing the Beta Process (BP), the Indian Buffet Process (IBP), and related sparseness-promoting techniques to infer a proper number of factors. The posterior density function on the model parameters is computed using Gibbs sampling and variational Bayesian (VB) analysis. Time-evolving gene-expression data are considered for respiratory syncytial virus (RSV), Rhino virus, and influenza, using blood samples from healthy human subjects. These data were acquired in three challenge studies, each executed after receiving institutional review board (IRB) approval from Duke University. Comparisons are made between several alternative means of per-forming nonparametric factor analysis on these data, with comparisons as well to sparse-PCA and Penalized Matrix Decomposition (PMD), closely related non-Bayesian approaches. Applying the Beta Process to the factor scores, or to the singular values of a pseudo-SVD construction, the proposed algorithms infer the number of factors in gene-expression data. For real data the "true" number of factors is unknown; in our simulations we consider a range of noise variances, and the proposed Bayesian models inferred the number of factors accurately relative to other methods in the literature, such as sparse-PCA and PMD. We have also identified a "pan-viral" factor of importance for each of the three viruses considered in this study. We have identified a set of genes associated with this pan-viral factor, of interest for early detection of such viruses based upon the host response, as quantified via gene-expression data.

The HVT technique and the 'uncertainty' relation for central potentials

NASA Astrophysics Data System (ADS)

Grypeos, M. E.; Koutroulos, C. G.; Oyewumi, K. J.; Petridou, Th

2004-08-01

The quantum mechanical hypervirial theorems (HVT) technique is used to treat the so-called 'uncertainty' relation for quite a general class of central potential wells, including the (reduced) Poeschl-Teller and the Gaussian one. It is shown that this technique is quite suitable in deriving an approximate analytic expression in the form of a truncated power series expansion for the dimensionless product Pnl equiv langr2rangnllangp2rangnl/planck2, for every (deeply) bound state of a particle moving non-relativistically in the well, provided that a (dimensionless) parameter s is sufficiently small. Attention is also paid to a number of cases, among the limited existing ones, in which exact analytic or semi-analytic expressions for Pnl can be derived. Finally, numerical results are given and discussed.

Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas.

PubMed

Etemadmoghadam, Dariush; deFazio, Anna; Beroukhim, Rameen; Mermel, Craig; George, Joshy; Getz, Gad; Tothill, Richard; Okamoto, Aikou; Raeder, Maria B; Harnett, Paul; Lade, Stephen; Akslen, Lars A; Tinker, Anna V; Locandro, Bianca; Alsop, Kathryn; Chiew, Yoke-Eng; Traficante, Nadia; Fereday, Sian; Johnson, Daryl; Fox, Stephen; Sellers, William; Urashima, Mitsuyoshi; Salvesen, Helga B; Meyerson, Matthew; Bowtell, David

2009-02-15

A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-based treatment. We analyzed somatic DNA copy number variation and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Genome-wide copy number variation was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate copy number variation to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of 12 candidate genes as independent validation of previously reported associations with clinical outcome. Likely copy number variation targets and tumor molecular subtypes were further characterized by gene expression profiling. Amplification of 19q12, containing cyclin E (CCNE1), and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor coactivator NCOA3, was significantly associated with poor response to primary treatment. Other genes previously associated with copy number variation and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too was a subset of treatment-responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification overexpressed genes involved in extracellular matrix deposition. We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer.

Analysis of heat transfer for unsteady MHD free convection flow of rotating Jeffrey nanofluid saturated in a porous medium

NASA Astrophysics Data System (ADS)

Mohd Zin, Nor Athirah; Khan, Ilyas; Shafie, Sharidan; Alshomrani, Ali Saleh

In this article, the influence of thermal radiation on unsteady magnetohydrodynamics (MHD) free convection flow of rotating Jeffrey nanofluid passing through a porous medium is studied. The silver nanoparticles (AgNPs) are dispersed in the Kerosene Oil (KO) which is chosen as conventional base fluid. Appropriate dimensionless variables are used and the system of equations is transformed into dimensionless form. The resulting problem is solved using the Laplace transform technique. The impact of pertinent parameters including volume fraction φ , material parameters of Jeffrey fluid λ1 , λ , rotation parameter r , Hartmann number Ha , permeability parameter K , Grashof number Gr , Prandtl number Pr , radiation parameter Rd and dimensionless time t on velocity and temperature profiles are presented graphically with comprehensive discussions. It is observed that, the rotation parameter, due to the Coriolis force, tends to decrease the primary velocity but reverse effect is observed in the secondary velocity. It is also observed that, the Lorentz force retards the fluid flow for both primary and secondary velocities. The expressions for skin friction and Nusselt number are also evaluated for different values of emerging parameters. A comparative study with the existing published work is provided in order to verify the present results. An excellent agreement is found.

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis.

PubMed

Soneson, Charlotte; Lilljebjörn, Henrik; Fioretos, Thoas; Fontes, Magnus

2010-04-15

With the rapid development of new genetic measurement methods, several types of genetic alterations can be quantified in a high-throughput manner. While the initial focus has been on investigating each data set separately, there is an increasing interest in studying the correlation structure between two or more data sets. Multivariate methods based on Canonical Correlation Analysis (CCA) have been proposed for integrating paired genetic data sets. The high dimensionality of microarray data imposes computational difficulties, which have been addressed for instance by studying the covariance structure of the data, or by reducing the number of variables prior to applying the CCA. In this work, we propose a new method for analyzing high-dimensional paired genetic data sets, which mainly emphasizes the correlation structure and still permits efficient application to very large data sets. The method is implemented by translating a regularized CCA to its dual form, where the computational complexity depends mainly on the number of samples instead of the number of variables. The optimal regularization parameters are chosen by cross-validation. We apply the regularized dual CCA, as well as a classical CCA preceded by a dimension-reducing Principal Components Analysis (PCA), to a paired data set of gene expression changes and copy number alterations in leukemia. Using the correlation-maximizing methods, regularized dual CCA and PCA+CCA, we show that without pre-selection of known disease-relevant genes, and without using information about clinical class membership, an exploratory analysis singles out two patient groups, corresponding to well-known leukemia subtypes. Furthermore, the variables showing the highest relevance to the extracted features agree with previous biological knowledge concerning copy number alterations and gene expression changes in these subtypes. Finally, the correlation-maximizing methods are shown to yield results which are more biologically

Changes in mast cell number and stem cell factor expression in human skin after radiotherapy for breast cancer.

PubMed

Westbury, Charlotte B; Freeman, Alex; Rashid, Mohammed; Pearson, Ann; Yarnold, John R; Short, Susan C

2014-05-01

Mast cells are involved in the pathogenesis of radiation fibrosis and may be a therapeutic target. The mechanism of increased mast cell number in relation to acute and late tissue responses in human skin was investigated. Punch biopsies of skin 1 and 15-18 months after breast radiotherapy and a contralateral control biopsy were collected. Mast cells were quantified by immunohistochemistry using the markers c-Kit and tryptase. Stem cell factor (SCF) and collagen-1 expression was analysed by qRT-PCR. Clinical photographic scores were performed at post-surgical baseline and 18 months and 5 years post-radiotherapy. Primary human dermal microvascular endothelial cell (HDMEC) cultures were exposed to 2Gy ionising radiation and p53 and SCF expression was analysed by Western blotting and ELISA. Dermal mast cell numbers were increased at 1 (p=0.047) and 18 months (p=0.040) using c-Kit, and at 18 months (p=0.024) using tryptase immunostaining. Collagen-1 mRNA in skin was increased at 1 month (p=0.047) and 18 months (p=0.032) and SCF mRNA increased at 1 month (p=0.003). None of 16 cases scored had a change in photographic appearance at 5 years, compared to baseline. SCF expression was not increased in HDMECs irradiated in vitro. Increased mast cell number was associated with up-regulated collagen-1 expression in human skin at early and late time points. This increase could be secondary to elevated SCF expression at 1 month after radiotherapy. Although mast cells accumulate around blood vessels, no endothelial cell secretion of SCF was seen after in vitro irradiation. Modification of mast cell number and collagen-1 expression may be observed in skin at 1 and 18 months after radiotherapy in breast cancer patients with no change in photographic breast appearance at 5 years. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

NASA Technical Reports Server (NTRS)

Woronowicz, Michael

2016-01-01

Analytical expressions for column number density (CND) are developed for optical line of sight paths through a variety of steady free molecule point source models including directionally-constrained effusion (Mach number M = 0) and flow from a sonic orifice (M = 1). Sonic orifice solutions are approximate, developed using a fair simulacrum fitted to the free molecule solution. Expressions are also developed for a spherically-symmetric thermal expansion (M = 0). CND solutions are found for the most general paths relative to these sources and briefly explored. It is determined that the maximum CND from a distant location through directed effusion and sonic orifice cases occurs along the path parallel to the source plane that intersects the plume axis. For the effusive case this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plume's axis. For sonic plumes this ratio is reduced to about 4/3. For high Mach number cases the maximum CND will be found along the axial centerline path. Keywords: column number density, plume flows, outgassing, free molecule flow.

SURFACE FISSURE FORMATION ABOVE UNDERGROUND COALSEAM FIRES: DIMENSIONLESS RELATIONSHIPS BETWEEN SURFACE FISSURES AND SUBSURFACE SUBSIDENCE

NASA Astrophysics Data System (ADS)

Ide, T. S.; Pollard, D. D.; Orr, F. M.

2009-12-01

that relationships exist between the surface displacement magnitudes and directions, and the subsurface subsidence due to coal combustion. Subsidence variables include the length, magnitude, depth and location of subsidence, as well as the weight of the overburden. Each of the four types of surface features was related to these subsurface subsidence variables using a set of dimensionless curves. The simulation results were validated with field measurements from a nearby outcrop and borehole drilling. The possibility of using InSAR data to further constrain these model results is being investigated. The simulated dimensionless curves establish a useful rules of thumb to aid the interpretation and mitigation of coal fires, since these curves can be used to relate a surface fissures aperture, an easily measurable parameter, to variables such as the magnitude of subsurface subsidence that are harder to observe

Empirical, dimensionless, cumulative-rainfall hyetographs developed from 1959-86 storm data for selected small watersheds in Texas

USGS Publications Warehouse

Williams-Sether, Tara; Asquith, William H.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

2004-01-01

A database of incremental cumulative-rainfall values for storms that occurred in small urban and rural watersheds in north and south central Texas during the period from 1959 to 1986 was used to develop empirical, dimensionless, cumulative-rainfall hyetographs. Storm-quartile classifications were determined from the cumulative-rainfall values, which were divided into data groups on the basis of storm-quartile classification (first, second, third, fourth, and first through fourth combined), storm duration (0 to 6, 6 to 12, 12 to 24, 24 to 72, and 0 to 72 hours), and rainfall amount (1 inch or more). Removal of long leading tails, in effect, shortened the storm duration and, in some cases, affected the storm-quartile classification. Therefore, two storm groups, untrimmed and trimmed, were used for analysis. The trimmed storms generally are preferred for interpretation. For a 12-hour or less trimmed storm duration, approximately 49 percent of the storms are first quartile. For trimmed storm durations of 12 to 24 and 24 to 72 hours, 47 and 38 percent, respectively, of the storms are first quartile. For a trimmed storm duration of 0 to 72 hours, the first-, second-, third-, and fourth-quartile storms accounted for 46, 21, 20, and 13 percent of all storms, respectively. The 90th-percentile curve for first-quartile storms indicated about 90 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for first-quartile storms indicated about 30 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 90th-percentile curve for fourth-quartile storms indicated about 33 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for fourth-quartile storms indicated less than 5 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. Statistics for the empirical, dimensionless

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

PubMed

Carpenter, Danielle; Mitchell, Laura M; Armour, John A L

2017-02-20

Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P < 0.0005) and enzyme activity (13.6% of variance, P < 0.0005) but did not explain the majority of observed variation between individuals. AMY1-odd and AMY1-even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant (P = 0.052). Production of salivary amylase is correlated with AMY1 CNV, but the majority of interindividual variation comes from other sources. Long-range haplotype structure may affect expression, but this was not significant in our data.

Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

PubMed

Iddawela, Mahesh; Rueda, Oscar; Eremin, Jenny; Eremin, Oleg; Cowley, Jed; Earl, Helena M; Caldas, Carlos

2017-07-11

An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide

Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters.

PubMed

Lukashin, A V; Fuchs, R

2001-05-01

Cluster analysis of genome-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and samples. In the present paper, we focus on several important issues related to clustering algorithms that have not yet been fully studied. We describe a simple and robust algorithm for the clustering of temporal gene expression profiles that is based on the simulated annealing procedure. In general, this algorithm guarantees to eventually find the globally optimal distribution of genes over clusters. We introduce an iterative scheme that serves to evaluate quantitatively the optimal number of clusters for each specific data set. The scheme is based on standard approaches used in regular statistical tests. The basic idea is to organize the search of the optimal number of clusters simultaneously with the optimization of the distribution of genes over clusters. The efficiency of the proposed algorithm has been evaluated by means of a reverse engineering experiment, that is, a situation in which the correct distribution of genes over clusters is known a priori. The employment of this statistically rigorous test has shown that our algorithm places greater than 90% genes into correct clusters. Finally, the algorithm has been tested on real gene expression data (expression changes during yeast cell cycle) for which the fundamental patterns of gene expression and the assignment of genes to clusters are well understood from numerous previous studies.

Rarefaction waves in van der Waals fluids with an arbitrary number of degrees of freedom

DOE PAGES

Yuen, Albert; Barnard, John J.

2015-09-30

The isentropic expansion of an instantaneously and homogeneously heated foil is calculated using a 1D fluid model. The initial temperature and density are assumed to be in the vicinity of the critical temperature and solid density, respectively. The fluid is assumed to satisfy the van der Waals equation of state with an arbitrary number of degrees of freedom. Self-similar Riemann solutions are found. With a larger number of degrees of freedom f, depending on the initial dimensionless entropymore » $$˜\\atop{s_0}$$, a richer family of foil expansion behaviors have been found. We calculate the domain in parameter space where these behaviors occur. In total, eight types of rarefaction waves are found and described.« less

On the applicability of low-dimensional models for convective flow reversals at extreme Prandtl numbers

NASA Astrophysics Data System (ADS)

Mannattil, Manu; Pandey, Ambrish; Verma, Mahendra K.; Chakraborty, Sagar

2017-12-01

Constructing simpler models, either stochastic or deterministic, for exploring the phenomenon of flow reversals in fluid systems is in vogue across disciplines. Using direct numerical simulations and nonlinear time series analysis, we illustrate that the basic nature of flow reversals in convecting fluids can depend on the dimensionless parameters describing the system. Specifically, we find evidence of low-dimensional behavior in flow reversals occurring at zero Prandtl number, whereas we fail to find such signatures for reversals at infinite Prandtl number. Thus, even in a single system, as one varies the system parameters, one can encounter reversals that are fundamentally different in nature. Consequently, we conclude that a single general low-dimensional deterministic model cannot faithfully characterize flow reversals for every set of parameter values.

[Abnormality of TOP2A expression and its gene copy number variations in neuroblastic tumors].

PubMed

Chen, J M; Zhou, C J; Ma, X L; Guan, D D; Yang, L Y; Yue, P; Gong, L P

2016-11-08

Objective: To detect TOP2A protein expression and gene copy number alterations, and to analyze related clinical and pathological implications in pediatric neuroblastic tumors (NT). Methods: Immunohistochemistry was used to detect TOP2A protein expression. Fluorescence in situ hybridization (FISH) was used to detect numerical aberrations of TOP2A. Results: TOP2A protein was expressed in 59.1%(52/88) of cases, which was associated with differentiation ( P =0.006), Ki-67 index ( P <0.01) and MKI ( P =0.001). Twenty-eight cases (35.0%, 28/88) showed TOP2A gene amplification, which was correlated with the age ( P <0.01), clinical stage ( P =0.028), high risk group ( P =0.001), Ki-67 index ( P =0.040) and differentiation ( P =0.014). Survival analysis showed that TOP2A expression was related to survival rate. Multivariate analyses showed that TOP2A expression was an independent predictor for poor prognosis ( P =0.010). Conclusions: More than half of the cases show TOP2A expression, which is more likely associated with NB, high Ki-67 index and high MKI. Cases with TOP2A expression have shorter survivals and poorer prognosis. TOP2A amplification is seen in 35% and likely occurs in patients older than 18 months and at advanced INSS stages (Ⅲ and Ⅳ). As a target of the anthracycline-based adjuvant drugs, TOP2A test can be used to select patient with NT for the therapy.

Integrative analysis of copy number and gene expression data suggests novel pathogenetic mechanisms in primary myelofibrosis.

PubMed

Salati, Simona; Zini, Roberta; Nuzzo, Simona; Guglielmelli, Paola; Pennucci, Valentina; Prudente, Zelia; Ruberti, Samantha; Rontauroli, Sebastiano; Norfo, Ruggiero; Bianchi, Elisa; Bogani, Costanza; Rotunno, Giada; Fanelli, Tiziana; Mannarelli, Carmela; Rosti, Vittorio; Salmoiraghi, Silvia; Pietra, Daniela; Ferrari, Sergio; Barosi, Giovanni; Rambaldi, Alessandro; Cazzola, Mario; Bicciato, Silvio; Tagliafico, Enrico; Vannucchi, Alessandro M; Manfredini, Rossella

2016-04-01

Primary myelofibrosis (PMF) is a Myeloproliferative Neoplasm (MPN) characterized by megakaryocyte hyperplasia, progressive bone marrow fibrosis, extramedullary hematopoiesis and transformation to Acute Myeloid Leukemia (AML). A number of phenotypic driver (JAK2, CALR, MPL) and additional subclonal mutations have been described in PMF, pointing to a complex genomic landscape. To discover novel genomic lesions that can contribute to disease phenotype and/or development, gene expression and copy number signals were integrated and several genomic abnormalities leading to a concordant alteration in gene expression levels were identified. In particular, copy number gain in the polyamine oxidase (PAOX) gene locus was accompanied by a coordinated transcriptional up-regulation in PMF patients. PAOX inhibition resulted in rapid cell death of PMF progenitor cells, while sparing normal cells, suggesting that PAOX inhibition could represent a therapeutic strategy to selectively target PMF cells without affecting normal hematopoietic cells' survival. Moreover, copy number loss in the chromatin modifier HMGXB4 gene correlates with a concomitant transcriptional down-regulation in PMF patients. Interestingly, silencing of HMGXB4 induces megakaryocyte differentiation, while inhibiting erythroid development, in human hematopoietic stem/progenitor cells. These results highlight a previously un-reported, yet potentially interesting role of HMGXB4 in the hematopoietic system and suggest that genomic and transcriptional imbalances of HMGXB4 could contribute to the aberrant expansion of the megakaryocytic lineage that characterizes PMF patients. © 2015 UICC.

Electromagneto squeezing rotational flow of Carbon (C)-Water (H2O) kerosene oil nanofluid past a Riga plate: A numerical study.

PubMed

Hayat, Tasawar; Khan, Mumtaz; Khan, Muhammad Ijaz; Alsaedi, Ahmed; Ayub, Muhammad

2017-01-01

This article predicts the electromagneto squeezing rotational flow of carbon-water nanofluid between two stretchable Riga plates. Riga plate is known as electromagnetic actuator which is the combination of permanent magnets and a span wise aligned array of alternating electrodes mounted on a plane surface. Mathematical model is developed for the flow problem with the phenomena of melting heat transfer, viscous dissipation and heat generation/absorption. Water and kerosene oil are utilized as the base fluids whereas single and multi-wall carbon nanotubes as the nanomaterials. Numerical solutions of the dimensionless problems are constructed by using built in shooting method. The correlation expressions for Nusselt number and skin friction coefficient are developed and examined through numerical data. Characteristics of numerous relevant parameters on the dimensionless temperature and velocity are sketched and discussed. Horizontal velocity is found to enhance for higher modified Hartman number.

The influence of liquid/vapor phase change onto the Nusselt number

NASA Astrophysics Data System (ADS)

Popescu, Elena-Roxana; Colin, Catherine; Tanguy, Sebastien

2017-11-01

In spite of its significant interest in various fields, there is currently a very few information on how an external flow will modify the evaporation or the condensation of a liquid surface. Although most applications involve turbulent flows, the simpler configuration where a laminar superheated or subcooled vapor flow is shearing a saturated liquid interface has still never been solved. Based on a numerical approach, we propose to characterize the interaction between a laminar boundary layer of a superheated or subcooled vapor flow and a static liquid pool at saturation temperature. By performing a full set of simulations sweeping the parameters space, correlations are proposed for the first time on the Nusselt number depending on the dimensionless numbers that characterize both vaporization and condensation. As attended, the Nusselt number decreases or increases in the configurations involving respectively vaporization or condensation. More unexpected is the behaviour of the friction of the vapor flow on the liquid pool, for which we report that it is weakly affected by the phase change, despite the important variation of the local flow structure due to evaporation or condensation.

Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

NASA Technical Reports Server (NTRS)

Woronowicz, Michael S.

2016-01-01

Analytical expressions for column number density (CND) are developed for optical line of sight paths through a variety of steady free molecule point source models including directionally-constrained effusion (Mach number M = 0) and flow from a sonic orifice (M 1). Sonic orifice solutions are approximate, developed using a fair simulacrum fitted to the free molecule solution. Expressions are also developed for a spherically-symmetric thermal expansion (M = 0). CND solutions are found for the most general paths relative to these sources and briefly explored. It is determined that the maximum CND from a distant location through directed effusion and sonic orifice cases occurs along the path parallel to the source plane that intersects the plume axis. For the effusive case this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plumes axis. For sonic plumes this ratio is reduced to about 43. For high Mach number cases the maximum CND will be found along the axial centerline path.

Maternal age and ovarian stimulation independently affect oocyte mtDNA copy number and cumulus cell gene expression in bovine clones.

PubMed

Cree, Lynsey M; Hammond, Elizabeth R; Shelling, Andrew N; Berg, Martin C; Peek, John C; Green, Mark P

2015-06-01

Does maternal ageing and ovarian stimulation alter mitochondrial DNA (mtDNA) copy number and gene expression of oocytes and cumulus cells from a novel bovine model for human IVF? Oocytes collected from females with identical nuclear genetics show decreased mtDNA copy number and increased expression of an endoplasmic reticulum (ER) stress gene with repect to ovarian stimulation, whilst differences in the expression of genes involved in mitochondrial function, antioxidant protection and apoptosis were evident in relation to maternal ageing and the degree of ovarian stimulation in cumulus cells. Oocyte quality declines with advancing maternal age; however, the underlying mechanism, as well as the effects of ovarian stimulation are poorly understood. Human studies investigating these effects are often limited by differences in age and ovarian stimulation regimens within a patient cohort, as well as genetic and environmental variability. A novel bovine cross-sectional maternal age model for human IVF was undertaken. Follicles were aspirated from young (3 years of age; n = 7 females) and old (10 years of age; n = 5 females) Holstein Freisian clones following multiple unstimulated, mild and standard ovarian stimulation cycles. These bovine cloned females were generated by the process of somatic cell nuclear transfer (SCNT) from the same founder and represent a homogeneous population with reduced genetic and environmental variability. Maternal age and ovarian stimulation effects were investigated in relation to mtDNA copy number, and the expression of 19 genes involved in mitochondrial function, antioxidant protection, oocyte-cumulus cell signalling and follicle development in both oocytes and cumulus cells. Young (3 years of age; n = 7 females) and old (10 years of age; n = 5 females) Holstein Freisian bovine clones were maintained as one herd. Stimulation cycles were based on the long GnRH agonist down-regulation regimen used in human fertility clinics. Follicle growth

A dimensionless ordered pull-through model of the mammalian lens epithelium evidences scaling across species and explains the age-dependent changes in cell density in the human lens

PubMed Central

Wu, Jun Jie; Wu, Weiju; Tholozan, Frederique M.; Saunter, Christopher D.; Girkin, John M.; Quinlan, Roy A.

2015-01-01

We present a mathematical (ordered pull-through; OPT) model of the cell-density profile for the mammalian lens epithelium together with new experimental data. The model is based upon dimensionless parameters, an important criterion for inter-species comparisons where lens sizes can vary greatly (e.g. bovine (approx. 18 mm); mouse (approx. 2 mm)) and confirms that mammalian lenses scale with size. The validated model includes two parameters: β/α, which is the ratio of the proliferation rate in the peripheral and in the central region of the lens; and γGZ, a dimensionless pull-through parameter that accounts for the cell transition and exit from the epithelium into the lens body. Best-fit values were determined for mouse, rat, rabbit, bovine and human lens epithelia. The OPT model accounts for the peak in cell density at the periphery of the lens epithelium, a region where cell proliferation is concentrated and reaches a maximum coincident with the germinative zone. The β/α ratio correlates with the measured FGF-2 gradient, a morphogen critical to lens cell survival, proliferation and differentiation. As proliferation declines with age, the OPT model predicted age-dependent changes in cell-density profiles, which we observed in mouse and human lenses. PMID:26236824

Generalized Knudsen Number for Unsteady Fluid Flow.

PubMed

Kara, V; Yakhot, V; Ekinci, K L

2017-02-17

We explore the scaling behavior of an unsteady flow that is generated by an oscillating body of finite size in a gas. If the gas is gradually rarefied, the Navier-Stokes equations begin to fail and a kinetic description of the flow becomes more appropriate. The failure of the Navier-Stokes equations can be thought to take place via two different physical mechanisms: either the continuum hypothesis breaks down as a result of a finite size effect or local equilibrium is violated due to the high rate of strain. By independently tuning the relevant linear dimension and the frequency of the oscillating body, we can experimentally observe these two different physical mechanisms. All the experimental data, however, can be collapsed using a single dimensionless scaling parameter that combines the relevant linear dimension and the frequency of the body. This proposed Knudsen number for an unsteady flow is rooted in a fundamental symmetry principle, namely, Galilean invariance.

Generalized Knudsen Number for Unsteady Fluid Flow

NASA Astrophysics Data System (ADS)

Kara, V.; Yakhot, V.; Ekinci, K. L.

2017-02-01

We explore the scaling behavior of an unsteady flow that is generated by an oscillating body of finite size in a gas. If the gas is gradually rarefied, the Navier-Stokes equations begin to fail and a kinetic description of the flow becomes more appropriate. The failure of the Navier-Stokes equations can be thought to take place via two different physical mechanisms: either the continuum hypothesis breaks down as a result of a finite size effect or local equilibrium is violated due to the high rate of strain. By independently tuning the relevant linear dimension and the frequency of the oscillating body, we can experimentally observe these two different physical mechanisms. All the experimental data, however, can be collapsed using a single dimensionless scaling parameter that combines the relevant linear dimension and the frequency of the body. This proposed Knudsen number for an unsteady flow is rooted in a fundamental symmetry principle, namely, Galilean invariance.

Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle.

PubMed

Zhang, Gui-Min; Zheng, Li; He, Hua; Song, Cheng-Chuang; Zhang, Zi-Jing; Cao, Xiu-Kai; Lei, Chu-Zhao; Lan, Xian-Yong; Qi, Xing-Lei; Chen, Hong; Huang, Yong-Zhen

2018-03-20

Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds. Though the GBP2 gene copy number presented no correlation with the transcriptional expression of JX (P > .05), but the transcriptional expression in heart is higher than other tissues, and the copy number in muscles and fat of JX is higher than others breeds. Statistical analysis revealed that the GBP2 gene CNV1 and CNV2 were significantly associated with growth traits (P < .05). In conclusion, this research established the correlations between CNVs of GBP2 gene and growth traits in different cattle breeds, and our results suggested that the CNVs in GBP2 gene may be considered markers for the molecular breeding of Chinese beef cattle. Copyright © 2018. Published by Elsevier B.V.

On the drag of model dendrite fragments at low Reynolds number

NASA Technical Reports Server (NTRS)

Zakhem, R.; Weidman, P. D.; Degroh, H. C., III

1993-01-01

An experimental study of low Reynolds number drag on laboratory models of dendrite fragments has been conducted. The terminal velocities of the dendrites undergoing free fall along their axis of symmetry were measured in a large Stokes flow facility. Corrections for wall interference give nearly linear drag vs Reynolds number curves. Corrections for both wall interference and inertia effects show that the dendrite Stokes settling velocities are always less than that of a sphere of equal mass and volume. In the Stokes limit, the settling speed ratio is found to correlate well with primary dendrite arm aspect ratio and a second dimensionless shape paremeter which serves as a measure of the fractal-like nature of the dendrite models. These results can be used to estimate equiaxed grain velocities and distance of travel in metal castings. The drag measurements may be used in numerical codes to calculate the movement of grains in a convecting melt in an effort to determine macrosegregation patterns caused by the sink/float mechanism.

Expression and copy number gains of the RET gene in 631 early and mid stage non‐small cell lung cancer cases

PubMed Central

Tan, Ling; Hu, Yerong; Tao, Yongguang; Wang, Bin; Xiao, Jun; Tang, Zhenjie; Lu, Ting

2018-01-01

Background To identify whether RET is a potential target for NSCLC treatment, we examined the status of the RET gene in 631 early and mid stage NSCLC cases from south central China. Methods RET expression was identified by Western blot. RET‐positive expression samples were verified by immunohistochemistry. RET gene mutation, copy number variation, and rearrangement were analyzed by DNA Sanger sequencing, TaqMan copy number assays, and reverse transcription‐PCR. ALK and ROS1 expression levels were tested by Western blot and EGFR mutation using Sanger sequencing. Results The RET‐positive rate was 2.5% (16/631). RET‐positive expression was related to poorer tumor differentiation (P < 0.05). In the 16 RET‐positive samples, only two samples of moderately and poorly differentiated lung adenocarcinomas displayed RET rearrangement, both in RET‐KIF5B fusion partners. Neither ALK nor ROS1 translocation was found. The EGFR mutation rate in RET‐positive samples was significantly lower than in RET‐negative samples (P < 0.05). Conclusion RET‐positive expression in early and mid stage NSCLC cases from south central China is relatively low and is related to poorer tumor differentiation. RET gene alterations (copy number gain and rearrangement) exist in all RET‐positive samples. RET‐positive expression is a relatively independent factor in NSCLC patients, which indicates that the RET gene may be a novel target site for personalized treatment of NSCLC. PMID:29473341

Details of Exact Low Prandtl Number Boundary-Layer Solutions for Forced and For Free Convection

NASA Technical Reports Server (NTRS)

Sparrow, E. M.; Gregg, J. L.

1959-01-01

A detailed report is given of exact (numerical) solutions of the laminar-boundary-layer equations for the Prandtl number range appropriate to liquid metals (0.003 to 0.03). Consideration is given to the following situations: (1) forced convection over a flat plate for the conditions of uniform wall temperature and uniform wall heat flux, and (2) free convection over an isothermal vertical plate. Tabulations of the new solutions are given in detail. Results are presented for the heat-transfer and shear-stress characteristics; temperature and velocity distributions are also shown. The heat-transfer results are correlated in terms of dimensionless parameters that vary only slightly over the entire liquid-metal range. Previous analytical and experimental work on low Prandtl number boundary layers is surveyed and compared with the new exact solutions.

Electromagneto squeezing rotational flow of Carbon (C)-Water (H2O) kerosene oil nanofluid past a Riga plate: A numerical study

PubMed Central

Hayat, Tasawar; Khan, Mumtaz; Alsaedi, Ahmed; Ayub, Muhammad

2017-01-01

This article predicts the electromagneto squeezing rotational flow of carbon-water nanofluid between two stretchable Riga plates. Riga plate is known as electromagnetic actuator which is the combination of permanent magnets and a span wise aligned array of alternating electrodes mounted on a plane surface. Mathematical model is developed for the flow problem with the phenomena of melting heat transfer, viscous dissipation and heat generation/absorption. Water and kerosene oil are utilized as the base fluids whereas single and multi-wall carbon nanotubes as the nanomaterials. Numerical solutions of the dimensionless problems are constructed by using built in shooting method. The correlation expressions for Nusselt number and skin friction coefficient are developed and examined through numerical data. Characteristics of numerous relevant parameters on the dimensionless temperature and velocity are sketched and discussed. Horizontal velocity is found to enhance for higher modified Hartman number. PMID:28813427

Hypoxia induces arginase II expression and increases viable human pulmonary artery smooth muscle cell numbers via AMPKα1 signaling

PubMed Central

Xue, Jianjing; Nelin, Leif D.

2017-01-01

Pulmonary artery smooth muscle cell (PASMC) proliferation is one of the hallmark features of hypoxia-induced pulmonary hypertension. With only supportive treatment options available for this life-threatening disease, treating and preventing the proliferation of PASMCs is a viable therapeutic option. A key promoter of hypoxia-induced increases in the number of viable human PASMCs is arginase II, with attenuation of viable cell numbers following pharmacologic inhibition or siRNA knockdown of the enzyme. Additionally, increased levels of arginase have been demonstrated in the pulmonary vasculature of patients with pulmonary hypertension. The signaling pathways responsible for the hypoxic induction of arginase II in PASMCs, however, remain unknown. Hypoxia is a recognized activator of AMPK, which is known to be expressed in human PASMCs (hPASMCs). Activation of AMPK by hypoxia has been shown to promote cell survival in PASMCs. In addition, pharmacologic agents targeting AMPK have been shown to attenuate chronic hypoxia-induced pulmonary hypertension in animal models. The present studies tested the hypothesis that hypoxia-induced arginase II expression in hPASMCs is mediated through AMPK signaling. We found that pharmacologic inhibitors of AMPK, as well as siRNA knockdown of AMPKα1, prevented hypoxia-induced arginase II. The hypoxia-induced increase in viable hPASMC numbers was also prevented following both pharmacologic inhibition and siRNA knockdown of AMPK. Furthermore, we demonstrate that overexpression of AMPK induced arginase II protein expression and viable cells numbers in hPASMCs. PMID:28213467

[Diagnostic value of MYB protein expression in adenoid cystic carcinoma and status of MYB gene copy number].

PubMed

Huo, Zhen; Zeng, Xuan; Wu, Shafei; Wu, Huanwen; Meng, Yunxiao; Liu, Yuanyuan; Luo, Yufeng; Cao, Jinling; Liang, Zhiyong

2015-08-01

To explore the diagnostic value of MYB protein expression for adenoid cystic carcinoma and its differential diagnosis from other salivary gland tumors, and to further investigate the status of MYB gene copy number. MYB expression was studied by immunohistochemistry in 34 adenoid cystic carcinomas, 55 non-adenoid cystic carcinomas (other salivary gland tumors) including 10 pleomorphic adenomas, 10 basal cell adenomas, 10 epithelial-myoepithelial carcinomas, 9 basal cell adenocarcinomas, 8 mucoepidermoid carcinomas, 4 carcinoma in pleomorphic adenomas, and 4 polymorphous low-grade adenocarcinoma. MYB gene copy number status was detected by FISH in MYB protein-positive cases. 82.4% (28/34) of adenoid cystic carcinomas were MYB protein-positive, compared with 9.1% (5/55) of non-adenoid cystic carcinomas, and the difference between the two groups was statistically significant (P < 0.01). 2/18 of adenoid cystic carcinomas had duplication of MYB gene by FISH, and all non-adenoid cystic carcinomas were negative although the difference was not statistically significant (P = 0.435). MYB protein expression is a useful diagnostic marker for adenoid cystic carcinomas in its separation from other salivary gland tumors. In addition, duplication of MYB gene is no a major mechanism for the MYB protein overexpression.

ALK gene copy number gain and immunohistochemical expression status using three antibodies in neuroblastoma.

PubMed

Kim, Eun Kyung; Kim, Sewha

2016-03-17

Anaplastic lymphoma kinase (ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC positive rate in ALK1 and 5A4 antibodies (p= < 0.001 and 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

ALK Gene Copy Number Gain and Immunohistochemical Expression Status Using Three Antibodies in Neuroblastoma.

PubMed

Kim, Eun Kyung; Kim, Sewha

2017-01-01

Anaplastic lymphoma kinase ( ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC-positive rate in ALK1 and 5A4 antibodies ( P < 0.001 and P = 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

PubMed Central

Lamarre, Sophie; Frasse, Pierre; Zouine, Mohamed; Labourdette, Delphine; Sainderichin, Elise; Hu, Guojian; Le Berre-Anton, Véronique; Bouzayen, Mondher; Maza, Elie

2018-01-01

RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression (DE) analysis. After a brief review of the main issues, methods and tools related to the DE analysis of RNA-Seq data, this article focuses on the impact of both the replicate number and library size in such analyses. While the main drawback of previous relevant studies is the lack of generality, we conducted both an analysis of a two-condition experiment (with eight biological replicates per condition) to compare the results with previous benchmark studies, and a meta-analysis of 17 experiments with up to 18 biological conditions, eight biological replicates and 100 million (M) reads per sample. As a global trend, we concluded that the replicate number has a larger impact than the library size on the power of the DE analysis, except for low-expressed genes, for which both parameters seem to have the same impact. Our study also provides new insights for practitioners aiming to enhance their experimental designs. For instance, by analyzing both the sensitivity and specificity of the DE analysis, we showed that the optimal threshold to control the false discovery rate (FDR) is approximately 2−r, where r is the replicate number. Furthermore, we showed that the false positive rate (FPR) is rather well controlled by all three studied R packages: DESeq, DESeq2, and edgeR. We also analyzed the impact of both the replicate number and library size on gene ontology (GO) enrichment analysis. Interestingly, we concluded that increases in the replicate number and library size tend to enhance the sensitivity and specificity, respectively, of the GO analysis. Finally, we recommend to RNA-Seq practitioners the production of a pilot data set to strictly analyze the power of their experimental design, or the use of a public data set, which should be similar to the data set they will obtain. For individuals working on tomato research

Deformation of ferrofluid marbles in the presence of a permanent magnet.

PubMed

Nguyen, Nam-Trung

2013-11-12

This paper investigates the deformation of ferrofluid marbles in the presence of a permanent magnet. Ferrofluid marbles are formed using a water-based ferrofluid and 1 μm hydrophobic polytetrafluoride particles. A marble placed on a Teflon coated glass plate deforms under gravity. In the presence of a permanent magnet, the marble is further deformed with a larger contact area. The geometric parameters are normalized by the radius of an undistorted spherical marble. The paper first discusses a scaling relationship between the dimensionless radius of the contact area as well as the dimensionless height and the magnetic Bond number. The dimensionless contact radius is proportional to the fourth root of the magnetic bond number. The dimensionless height scales with the inverse square root of the magnetic Bond number. In the case of a moving marble dragged by a permanent magnet, the deformation is evaluated as the difference between advancing and receding curvatures of the top view. The dimensionless height and the contact diameter of the marble do not significantly depend on the speed or the capillary number. The scaling analysis and experimental data show that the deformation is proportional to the capillary number.

Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum.

PubMed

Dietz-Pfeilstetter, Antje; Arndt, Nicola; Manske, Ulrike

2016-04-01

Transgenes in genetically modified plants are often not reliably expressed during development or in subsequent generations. Transcriptional gene silencing (TGS) as well as post-transcriptional gene silencing (PTGS) have been shown to occur in transgenic plants depending on integration pattern, copy number and integration site. In an effort to reduce position effects, to prevent read-through transcription and to provide a more accessible chromatin structure, a P35S-ß-glucuronidase (P35S-gus) transgene flanked by a scaffold/matrix attachment region from petunia (Petun-SAR), was introduced in Nicotiana tabacum plants by Agrobacterium tumefaciens mediated transformation. It was found that Petun-SAR mediates enhanced expression and copy number dependency up to 2 gene copies, but did not prevent gene silencing in transformants with multiple and rearranged gene copies. However, in contrast to the non-SAR transformants where silencing was irreversible and proceeded during long-term vegetative propagation and in progeny plants, gus expression in Petun-SAR plants was re-established in the course of development. Gene silencing was not necessarily accompanied by DNA methylation, while the gus transgene could still be expressed despite considerable CG methylation within the coding region.

Exploratory factor analysis of pathway copy number data with an application towards the integration with gene expression data.

PubMed

van Wieringen, Wessel N; van de Wiel, Mark A

2011-05-01

Realizing that genes often operate together, studies into the molecular biology of cancer shift focus from individual genes to pathways. In order to understand the regulatory mechanisms of a pathway, one must study its genes at all molecular levels. To facilitate such study at the genomic level, we developed exploratory factor analysis for the characterization of the variability of a pathway's copy number data. A latent variable model that describes the call probability data of a pathway is introduced and fitted with an EM algorithm. In two breast cancer data sets, it is shown that the first two latent variables of GO nodes, which inherit a clear interpretation from the call probabilities, are often related to the proportion of aberrations and a contrast of the probabilities of a loss and of a gain. Linking the latent variables to the node's gene expression data suggests that they capture the "global" effect of genomic aberrations on these transcript levels. In all, the proposed method provides an possibly insightful characterization of pathway copy number data, which may be fruitfully exploited to study the interaction between the pathway's DNA copy number aberrations and data from other molecular levels like gene expression.

I-Love relations for irrotational stars

NASA Astrophysics Data System (ADS)

Delsate, Térence

2015-12-01

In this short paper, we investigate the existence of universal relations between the gravimagnetic Love number of irrotational stars and the dimensionless moment of inertia. These Love numbers take into account the internal motion of the fluid, while the star is globally irrotational. The goal is to extend the so-called I-Love-Q relations—providing a strong correlation between the gravitoelectric Love number, the dimensionless moment of inertia and the dimensionless rotation-induced quadrupole—to the gravitomagnetic sector, where internal motion is taken into account. As a byproduct, we present for the first time this new gravitomagnetic Love number for realistic equations of state.

Low temperature-induced DNA hypermethylation attenuates expression of RhAG, an AGAMOUS homolog, and increases petal number in rose (Rosa hybrida).

PubMed

Ma, Nan; Chen, Wen; Fan, Tiangang; Tian, Yaran; Zhang, Shuai; Zeng, Daxing; Li, Yonghong

2015-10-05

Flower development is central to angiosperm reproduction and is regulated by a broad range of endogenous and exogenous stimuli. It has been well documented that ambient temperature plays a key role in controlling flowering time; however, the mechanisms by which temperature regulates floral organ differentiation remain largely unknown. In this study, we show that low temperature treatment significantly increases petal number in rose (Rosa hybrida) through the promotion of stamen petaloidy. Quantitative RT-PCR analysis revealed that the expression pattern of RhAG, a rose homolog of the Arabidopsis thaliana AGAMOUS C-function gene, is associated with low temperature regulated flower development. Silencing of RhAG mimicked the impact of low temperature treatments on petal development by significantly increasing petal number through an increased production of petaloid stamens. In situ hybridization studies further revealed that low temperature restricts its spatial expression area. Analysis of DNA methylation level showed that low temperature treatment enhances the methylation level of the RhAG promoter, and a specific promoter region that was hypermethylated at CHH loci under low temperature conditions, was identified by bisulfite sequencing. This suggests that epigenetic DNA methylation contributes to the ambient temperature modulation of RhAG expression. Our results provide highlights in the role of RhAG gene in petal number determination and add a new layer of complexity in the regulation of floral organ development. We propose that RhAG plays an essential role in rose flower patterning by regulating petal development, and that low temperatures increase petal number, at least in part, by suppressing RhAG expression via enhancing DNA CHH hypermethylation of the RhAG promoter.

Integrated Analysis of Genome-wide Copy Number Alterations and Gene Expression in MSS, CIMP-negative Colon Cancer

PubMed Central

Loo, Lenora WM; Tiirikainen, Maarit; Cheng, Iona; Lum-Jones, Annette; Seifried, Ann; Church, James M; Gryfe, Robert; Weisenberger, Daniel J; Lindor, Noralane M; Gallinger, Steven; Haile, Robert W; Duggan, David J; Thibodeau, Stephen N; Casey, Graham; Le Marchand, Loïc

2014-01-01

Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P<0.0001 and ±1.5 fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L and PRPF6) that were up-regulated and demonstrated a significant linear correlation (P<0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer. PMID:23341073

Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR.

PubMed

Jahn, Michael; Vorpahl, Carsten; Hübschmann, Thomas; Harms, Hauke; Müller, Susann

2016-12-19

Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in

On hydrologic similarity: A dimensionless flood frequency model using a generalized geomorphologic unit hydrograph and partial area runoff generation

NASA Technical Reports Server (NTRS)

Sivapalan, Murugesu; Wood, Eric F.; Beven, Keith J.

1993-01-01

One of the shortcomings of the original theory of the geomorphologic unit hydrograph (GUH) is that it assumes that runoff is generated uniformly from the entire catchment area. It is now recognized that in many catchments much of the runoff during storm events is produced on partial areas which usually form on narrow bands along the stream network. A storm response model that includes runoff generation on partial areas by both Hortonian and Dunne mechanisms was recently developed by the authors. In this paper a methodology for integrating this partial area runoff generation model with the GUH-based runoff routing model is presented; this leads to a generalized GUH. The generalized GUH and the storm response model are then used to estimate physically based flood frequency distributions. In most previous work the initial moisture state of the catchment had been assumed to be constant for all the storms. In this paper we relax this assumption and allow the initial moisture conditions to vary between storms. The resulting flood frequency distributions are cast in a scaled dimensionless framework where issues such as catchment scale and similarity can be conveniently addressed. A number of experiments are performed to study the sensitivity of the flood frequency response to some of the 'similarity' parameters identified in this formulation. The results indicate that one of the most important components of the derived flood frequency model relates to the specification of processes within the runoff generation model; specifically the inclusion of both saturation excess and Horton infiltration excess runoff production mechanisms. The dominance of these mechanisms over different return periods of the flood frequency distribution can significantly affect the distributional shape and confidence limits about the distribution. Comparisons with observed flood distributions seem to indicate that such mixed runoff production mechanisms influence flood distribution shape. The

MYC, FBXW7 and TP53 copy number variation and expression in Gastric Cancer

PubMed Central

2013-01-01

Background MYC deregulation is a common event in gastric carcinogenesis, usually as a consequence of gene amplification, chromosomal translocations, or posttranslational mechanisms. FBXW7 is a p53-controlled tumor-suppressor that plays a role in the regulation of cell cycle exit and reentry via MYC degradation. Methods We evaluated MYC, FBXW7, and TP53 copy number, mRNA levels, and protein expression in gastric cancer and paired non-neoplastic specimens from 33 patients and also in gastric adenocarcinoma cell lines. We also determined the invasion potential of the gastric cancer cell lines. Results MYC amplification was observed in 51.5% of gastric tumor samples. Deletion of one copy of FBXW7 and TP53 was observed in 45.5% and 21.2% of gastric tumors, respectively. MYC mRNA expression was significantly higher in tumors than in non-neoplastic samples. FBXW7 and TP53 mRNA expression was markedly lower in tumors than in paired non-neoplastic specimens. Moreover, deregulated MYC and FBXW7 mRNA expression was associated with the presence of lymph node metastasis and tumor stage III-IV. Additionally, MYC immunostaining was more frequently observed in intestinal-type than diffuse-type gastric cancers and was associated with MYC mRNA expression. In vitro studies showed that increased MYC and reduced FBXW7 expression is associated with a more invasive phenotype in gastric cancer cell lines. This result encouraged us to investigate the activity of the gelatinases MMP-2 and MMP-9 in both cell lines. Both gelatinases are synthesized predominantly by stromal cells rather than cancer cells, and it has been proposed that both contribute to cancer progression. We observed a significant increase in MMP-9 activity in ACP02 compared with ACP03 cells. These results confirmed that ACP02 cells have greater invasion capability than ACP03 cells. Conclusion In conclusion, FBXW7 and MYC mRNA may play a role in aggressive biologic behavior of gastric cancer cells and may be a useful

Thermal convection in a cylindrical enclosure

NASA Astrophysics Data System (ADS)

Shukla, K. N.

2005-02-01

The paper highlights the onset of convection in a fluid layer partially filled in an axisymmetric container. The equilibrium of the fluid is disturbed with the deformation of the interface due to residual acceleration. The general problem of deformable interface involves a dimensionless parameter, the Bond number. An analytical expression for the natural frequencies of the deformable surface is derived in terms of the Bond number, which determines the time period required for the stable location of the fluid for the propellant management of the spacecraft.

Mobility of power-law and Carreau fluids through fibrous media.

PubMed

Shahsavari, Setareh; McKinley, Gareth H

2015-12-01

The flow of generalized Newtonian fluids with a rate-dependent viscosity through fibrous media is studied, with a focus on developing relationships for evaluating the effective fluid mobility. Three methods are used here: (i) a numerical solution of the Cauchy momentum equation with the Carreau or power-law constitutive equations for pressure-driven flow in a fiber bed consisting of a periodic array of cylindrical fibers, (ii) an analytical solution for a unit cell model representing the flow characteristics of a periodic fibrous medium, and (iii) a scaling analysis of characteristic bulk parameters such as the effective shear rate, the effective viscosity, geometrical parameters of the system, and the fluid rheology. Our scaling analysis yields simple expressions for evaluating the transverse mobility functions for each model, which can be used for a wide range of medium porosity and fluid rheological parameters. While the dimensionless mobility is, in general, a function of the Carreau number and the medium porosity, our results show that for porosities less than ɛ≃0.65, the dimensionless mobility becomes independent of the Carreau number and the mobility function exhibits power-law characteristics as a result of the high shear rates at the pore scale. We derive a suitable criterion for determining the flow regime and the transition from a constant viscosity Newtonian response to a power-law regime in terms of a new Carreau number rescaled with a dimensionless function which incorporates the medium porosity and the arrangement of fibers.

Multiplex titration RT-PCR: rapid determination of gene expression patterns for a large number of genes

NASA Technical Reports Server (NTRS)

Nebenfuhr, A.; Lomax, T. L.

1998-01-01

We have developed an improved method for determination of gene expression levels with RT-PCR. The procedure is rapid and does not require extensive optimization or densitometric analysis. Since the detection of individual transcripts is PCR-based, small amounts of tissue samples are sufficient for the analysis of expression patterns in large gene families. Using this method, we were able to rapidly screen nine members of the Aux/IAA family of auxin-responsive genes and identify those genes which vary in message abundance in a tissue- and light-specific manner. While not offering the accuracy of conventional semi-quantitative or competitive RT-PCR, our method allows quick screening of large numbers of genes in a wide range of RNA samples with just a thermal cycler and standard gel analysis equipment.

Characterizing overwater roughness Reynolds number during hurricanes

NASA Astrophysics Data System (ADS)

Hsu, S. A.; Shen, Hui; He, Yijun

2017-11-01

The Reynolds number, which is the dimensionless ratio of the inertial force to the viscous force, is of great importance in the theory of hydrodynamic stability and the origin of turbulence. To investigate aerodynamically rough flow over a wind sea, pertinent measurements of wind and wave parameters from three data buoys during Hurricanes Kate, Lili, Ivan, Katrina, Rita, and Wilma are analyzed. It is demonstrated that wind seas prevail when the wind speed at 10 m and the wave steepness exceed 9 m s-1 and 0.020, respectively. It is found that using a power law the roughness Reynolds number is statistically significantly related to the significant wave height instead of the wind speed as used in the literature. The reason for this characterization is to avoid any self-correlation between Reynolds number and the wind speed. It is found that although most values of R_{*} were below 500, they could reach to approximately 1000 near the radius of maximum wind. It is shown that, when the significant wave height exceeds approximately 2 m in a wind sea, the air flow over that wind sea is already under the fully rough condition. Further analysis of simultaneous measurements of wind and wave parameters using the logarithmic law indicates that the estimated overwater friction velocity is consistent with other methods including the direct (eddy-covariance flux) measurements, the atmospheric vorticity approach, and the sea-surface current measurements during four slow moving super typhoons with wind speed up to 70 m s-1.

Kif3a Controls Murine Nephron Number Via GLI3 Repressor, Cell Survival, and Gene Expression in a Lineage-Specific Manner

PubMed Central

Chi, Lijun; Galtseva, Alevtina; Chen, Lin; Mo, Rong; Hui, Chi-chung; Rosenblum, Norman D.

2013-01-01

The primary cilium is required during early embryo patterning, epithelial tubulogenesis, and growth factor-dependent signal transduction. The requirement for primary cilia during renal epithelial-mesenchymal tissue interactions that give rise to nephrons is undefined. Here, we used Cre-mediated recombination to generate mice with Kif3a deficiency targeted to the ureteric and/or metanephric mesenchyme cell lineages in the embryonic kidney. Gradual loss of primary cilia in either lineage leads to a phenotype of reduced nephron number. Remarkably, in addition to cyst formation, loss of primary cilia in the ureteric epithelial cell leads to decreased expression of Wnt11 and Ret and reduced ureteric branching. Constitutive expression of GLI3 repressor (Gli3Δ699/+) rescues these abnormalities. In embryonic metanephric mesenchyme cells, Kif3a deficiency limits survival of nephrogenic progenitor cells and expression of genes required for nephron formation. Together, our data demonstrate that Kif3a controls nephron number via distinct cell lineage-specific mechanisms. PMID:23762375

GIS characterization of spatially distributed lifeline damage

USGS Publications Warehouse

Toprak, Selcuk; O'Rourke, Thomas; Tutuncu, Ilker

1999-01-01

This paper describes the visualization of spatially distributed water pipeline damage following an earthquake using geographical information systems (GIS). Pipeline damage is expressed as a repair rate (RR). Repair rate contours are developed with GIS by dividing the study area into grid cells (n ?? n), determining the number of particular pipeline repairs in each grid cell, and dividing the number of repairs by the length of that pipeline in each cell area. The resulting contour plot is a two-dimensional visualization of point source damage. High damage zones are defined herein as areas with an RR value greater than the mean RR for the entire study area of interest. A hyperbolic relationship between visual display of high pipeline damage zones and grid size, n, was developed. The relationship is expressed in terms of two dimensionless parameters, threshold area coverage (TAC) and dimensionless grid size (DGS). The relationship is valid over a wide range of different map scales spanning approximately 1,200 km2 for the largest portion of the Los Angeles water distribution system to 1 km2 for the Marina in San Francisco. This relationship can aid GIS users to get sufficiently refined, but easily visualized, maps of damage patterns.

Thyroid hormones increase stomach goblet cell numbers and mucin expression during indomethacin induced ulcer healing in Wistar rats.

PubMed

Namulema, Jackline; Nansunga, Miriam; Kato, Charles Drago; Kalange, Muhammudu; Olaleye, Samuel Babafemi

2018-01-01

Gastric ulcers are mucosal discontinuities that may extend into the mucosa, submucosa or even deeper. They result from an imbalance between mucosal aggressors and protective mechanisms that include the mucus bicarbonate layer. Thyroid hormones have been shown to accelerate gastric ulcer healing in part by increasing the adherent mucus levels. However, the effects of thyroid hormones on goblet cell numbers and expression of neutral and acidic mucins during ulcer healing have not been investigated. Thirty six adult male Wistar rats were randomly divided into six groups each with six animals. Group 1 (normal control) and group 2 (negative control) were given normal saline for eight weeks. Groups 3 and 4 were given 100 μg/kg per day per os of thyroxine so as to induce hyperthyroidism. Groups 5 and 6 received 0.01% ( w / v ) Propylthiouracil (PTU) for 8 weeks so as to induce hypothyroidism. After thyroid hormonal levels were confirmed using radioimmunoassay and immunoradiometric assays, ulcer induction was done using 40 mg/kg intragastric single dose of Indomethacin in groups 2, 3 and 5. Stomachs were extracted after day 3 and 7 of ulcer induction for histological examination. Histochemistry was carried out using Periodic Acid Shiff and Alcian Blue. The number of acidic and neutral goblet cells were determined by counting numbers per field. Mucin expression (%) was determined using Quick Photo Industrial software version 3.1. The numbers of neutral goblet cells (cells/field) increased significantly ( P  < 0.05) in the ulcer+thyroxine (14.67 ± 0.33), thyroxine (17.04 ± 1.71) and ulcer+PTU (12.89 ± 1.06) groups compared to the normal control (10.78 ± 1.07) at day 3. For the acidic goblet cells, differences between treatment groups were more pronounced at day 7 between the ulcer+thyroxine (22.56 ± 1.26) and thyroxine (22.89 ± 0.80). We further showed that percentage expression of both neutral and acidic mucins was significantly higher

Relaxation-type nonlocal inertial-number rheology for dry granular flows

NASA Astrophysics Data System (ADS)

Lee, Keng-lin; Yang, Fu-ling

2017-12-01

We propose a constitutive model to describe the nonlocality, hysteresis, and several flow features of dry granular materials. Taking the well-known inertial number I as a measure of sheared-induced local fluidization, we derive a relaxation model for I according to the evolution of microstructure during avalanche and dissipation processes. The model yields a nonmonotonic flow law for a homogeneous flow, accounting for hysteretic solid-fluid transition and intermittency in quasistatic flows. For an inhomogeneous flow, the model predicts a generalized Bagnold shear stress revealing the interplay of two microscopic nonlocal mechanisms: collisions among correlated structures and the diffusion of fluidization within the structures. In describing a uniform flow down an incline, the model reproduces the hysteretic starting and stopping heights and the Pouliquen flow rule for mean velocity. Moreover, a dimensionless parameter reflecting the nonlocal effect on the flow is discovered, which controls the transition between Bagnold and creeping flow dynamics.

Influence of sex on the number of circulating endothelial microparticles and microRNA expression in middle-aged adults.

PubMed

Bammert, Tyler D; Hijmans, Jamie G; Kavlich, Philip J; Lincenberg, Grace M; Reiakvam, Whitney R; Fay, Ryan T; Greiner, Jared J; Stauffer, Brian L; DeSouza, Christopher A

2017-08-01

What is the central question of this study? Are there sex-related differences in the number of circulating endothelial microparticles (EMPs) and microparticle microRNA expression in middle-aged adult humans? What is the main finding and its importance? Although the numbers of circulating endothelial microparticles do not differ between middle-aged men and women, there are sex-related differences in the expression of miR-125a in activation-derived EMPs and miR-34a in apoptosis-derived EMPs. Differences in circulating endothelial microparticle microRNA content may provide new insight into the sex-related disparity in the risk and prevalence of vascular disease in middle-aged adults. The aims of this study were to determine: (i) whether circulating concentrations of endothelial microparticles (EMPs) differ in middle-aged men compared with women; and (ii) whether there are sex-related differences in microRNA expression in EMPs. Peripheral blood was collected from 30 sedentary adults: 15 men (56 ± 6 years old) and 15 women (56 ± 5 years old). Endothelial microparticles were defined by markers of activation (CD62e + ) or apoptosis (CD31 + /CD42b - ) by flow cytometry. Expression of microRNA (miR-34a, 92a, 125a and 126) in activation- and apoptosis-derived EMPs was measured by RT-PCR. Circulating activation- (33 ± 31 versus 39 ± 35 microparticles μl -1 ) and apoptosis-derived EMPs (49 ± 54 versus 42 ± 43 microparticles μl -1 ) were not significantly different between men and women. Expression of miR-125a (2.23 ± 2.01 versus 6.95 ± 3.99 a.u.) was lower (∼215%; P < 0.05) in activation-derived EMPs, whereas expression of miR-34a (1.17 ± 1.43 versus 0.38 ± 0.35 a.u.) was higher (∼210%; P < 0.05) in apoptosis-derived EMPs from men compared with women. Expression of microRNA in circulating EMPs may provide new insight into sex-related differences in cardiovascular disease. © 2017 The Authors. Experimental Physiology © 2017 The

Age-Dependent Brain Gene Expression and Copy Number Anomalies in Autism Suggest Distinct Pathological Processes at Young Versus Mature Ages

PubMed Central

Winn, Mary E.; Barnes, Cynthia Carter; Li, Hai-Ri; Weiss, Lauren; Fan, Jian-Bing; Murray, Sarah; April, Craig; Belinson, Haim; Fu, Xiang-Dong; Wynshaw-Boris, Anthony; Schork, Nicholas J.; Courchesne, Eric

2012-01-01

Autism is a highly heritable neurodevelopmental disorder, yet the genetic underpinnings of the disorder are largely unknown. Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association, linkage, and expression studies have not identified genetic factors that explain this trajectory. Few studies have had sufficient statistical power to investigate whole-genome gene expression and genotypic variation in the autistic brain, especially in regions that display the greatest growth abnormality. Previous functional genomic studies have identified possible alterations in transcript levels of genes related to neurodevelopment and immune function. Thus, there is a need for genetic studies involving key brain regions to replicate these findings and solidify the role of particular functional pathways in autism pathogenesis. We therefore sought to identify abnormal brain gene expression patterns via whole-genome analysis of mRNA levels and copy number variations (CNVs) in autistic and control postmortem brain samples. We focused on prefrontal cortex tissue where excess neuron numbers and cortical overgrowth are pronounced in the majority of autism cases. We found evidence for dysregulation in pathways governing cell number, cortical patterning, and differentiation in young autistic prefrontal cortex. In contrast, adult autistic prefrontal cortex showed dysregulation of signaling and repair pathways. Genes regulating cell cycle also exhibited autism-specific CNVs in DNA derived from prefrontal cortex, and these genes were significantly associated with autism in genome-wide association study datasets. Our results suggest that CNVs and age-dependent gene expression changes in autism may reflect distinct pathological processes in the developing versus the mature autistic prefrontal cortex. Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons

Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages.

PubMed

Chow, Maggie L; Pramparo, Tiziano; Winn, Mary E; Barnes, Cynthia Carter; Li, Hai-Ri; Weiss, Lauren; Fan, Jian-Bing; Murray, Sarah; April, Craig; Belinson, Haim; Fu, Xiang-Dong; Wynshaw-Boris, Anthony; Schork, Nicholas J; Courchesne, Eric

2012-01-01

Autism is a highly heritable neurodevelopmental disorder, yet the genetic underpinnings of the disorder are largely unknown. Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association, linkage, and expression studies have not identified genetic factors that explain this trajectory. Few studies have had sufficient statistical power to investigate whole-genome gene expression and genotypic variation in the autistic brain, especially in regions that display the greatest growth abnormality. Previous functional genomic studies have identified possible alterations in transcript levels of genes related to neurodevelopment and immune function. Thus, there is a need for genetic studies involving key brain regions to replicate these findings and solidify the role of particular functional pathways in autism pathogenesis. We therefore sought to identify abnormal brain gene expression patterns via whole-genome analysis of mRNA levels and copy number variations (CNVs) in autistic and control postmortem brain samples. We focused on prefrontal cortex tissue where excess neuron numbers and cortical overgrowth are pronounced in the majority of autism cases. We found evidence for dysregulation in pathways governing cell number, cortical patterning, and differentiation in young autistic prefrontal cortex. In contrast, adult autistic prefrontal cortex showed dysregulation of signaling and repair pathways. Genes regulating cell cycle also exhibited autism-specific CNVs in DNA derived from prefrontal cortex, and these genes were significantly associated with autism in genome-wide association study datasets. Our results suggest that CNVs and age-dependent gene expression changes in autism may reflect distinct pathological processes in the developing versus the mature autistic prefrontal cortex. Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons

Effect of aflatoxin B₁ on IgA⁺ cell number and immunoglobulin mRNA expression in the intestine of broilers.

PubMed

Jiang, Min; Fang, Jing; Peng, Xi; Cui, Hengmin; Yu, Zhengqiang

2015-01-01

Aflatoxin B1 (AFB1) is the most toxic group of mycotoxins produced by two species of the Aspergillus, common contaminants of food and animal feed. The purpose of our study was to determine the effect of AFB1 on the number of IgA(+) cell and immunoglobulin mRNA expression in the intestine of broilers. One hundred and fifty six one-day-old healthy Cobb broilers were randomly divided into the control group (the dosage of 0 mg/kg AFB1) and AFB1 group (the dosage of 0.6 mg/kg AFB1) with three replicates per group and 26 birds per replicate for 21 days, respectively. After necropsy at 7, 14 and 21 days of age, duodenum, jejunum and ileum samples were taken for analyzing IgA(+) cell by immunohistochemistry and IgA, pIgR, IgM and IgG mRNA expression by qRT-PCR. IgA(+) cells were mainly distributed in the lamina propria of small intestinal mucosa in both groups at 14 and 21 days of age. A significant decrease in the number of IgA(+) cells in the duodenum, jejunum and ileum was revealed in the AFB1 group compared with that of the control group. The expression levels of IgA, pIgR, IgM and IgG mRNA in the intestinal mucosa were lower in the AFB1 group than those in the control group at 14 and 21 days of age. Our data demonstrated that the dosage of 0.6 mg/kg AFB1 in broiler diet reduced the number of IgA(+) cell and the expression of IgA, pIgR, IgM and IgG mRNA in the small intestine.

Parvalbumin and neuropeptide Y expressing hippocampal GABA-ergic inhibitory interneuron numbers decline in a model of Gulf War illness.

PubMed

Megahed, Tarick; Hattiangady, Bharathi; Shuai, Bing; Shetty, Ashok K

2014-01-01

Cognitive dysfunction is amongst the most conspicuous symptoms in Gulf War illness (GWI). Combined exposure to the nerve gas antidote pyridostigmine bromide (PB), pesticides and stress during the Persian Gulf War-1 (PGW-1) are presumed to be among the major causes of GWI. Indeed, our recent studies in rat models have shown that exposure to GWI-related (GWIR) chemicals and mild stress for 4 weeks engenders cognitive impairments accompanied with several detrimental changes in the hippocampus. In this study, we tested whether reduced numbers of hippocampal gamma-amino butyric acid (GABA)-ergic interneurons are among the pathological changes induced by GWIR-chemicals and stress. Animals were exposed to low doses of GWIR-chemicals and mild stress for 4 weeks. Three months after this exposure, subpopulations of GABA-ergic interneurons expressing the calcium binding protein parvalbumin (PV), the neuropeptide Y (NPY) and somatostatin (SS) in the hippocampus were stereologically quantified. Animals exposed to GWIR-chemicals and stress for 4 weeks displayed reduced numbers of PV-expressing GABA-ergic interneurons in the dentate gyrus and NPY-expressing interneurons in the CA1 and CA3 subfields. However, no changes in SS+ interneuron population were observed in the hippocampus. Furthermore, GABA-ergic interneuron deficiency in these animals was associated with greatly diminished hippocampus neurogenesis. Because PV+ and NPY+ interneurons play roles in maintaining normal cognitive function and neurogenesis, and controlling the activity of excitatory neurons in the hippocampus, reduced numbers of these interneurons may be one of the major causes of cognitive dysfunction and reduced neurogenesis observed in GWI. Hence, strategies that improve inhibitory neurotransmission in the hippocampus may prove beneficial for reversing cognitive dysfunction in GWI.

Series of Reciprocal Triangular Numbers

ERIC Educational Resources Information Center

Bruckman, Paul; Dence, Joseph B.; Dence, Thomas P.; Young, Justin

2013-01-01

Reciprocal triangular numbers have appeared in series since the very first infinite series were summed. Here we attack a number of subseries of the reciprocal triangular numbers by methodically expressing them as integrals.

Maintenance of mitochondrial DNA copy number and expression are essential for preservation of mitochondrial function and cell growth.

PubMed

Jeng, Jaan-Yeh; Yeh, Tien-Shun; Lee, Jing-Wen; Lin, Shyh-Hsiang; Fong, Tsorng-Han; Hsieh, Rong-Hong

2008-02-01

To examine whether a reduction in the mtDNA level will compromise mitochondrial biogenesis and mitochondrial function, we created a cell model with depleted mtDNA. Stable transfection of small interfering (si)RNA of mitochondrial transcription factor A (Tfam) was used to interfere with Tfam gene expression. Selected stable clones showed 60-95% reduction in Tfam gene expression and 50-90% reduction in cytochrome b (Cyt b) gene expression. Tfam gene knockdown clones also showed decreased mtDNA-encoded cytochrome c oxidase subunit I (COX I) protein expression. However, no significant differences in protein expression were observed in nuclear DNA (nDNA)-encoded mitochondrial respiratory enzyme subunits. The cell morphology changed from a rhombus-like to a spindle-like form as determined in clones with decreased expressions of Tfam, mtRNA, and mitochondrial proteins. The mitochondrial respiratory enzyme activities and ATP production in such clones were significantly lower. The proportions of mtDNA mutations including 8-hydroxy-2'-deoxyguanosine (8-OHdG), a 4,977-bp deletion, and a 3,243-point mutation were also examined in these clones. No obvious increase in mtDNA mutations was observed in mitochondrial dysfunctional cell clones. The mitochondrial respiratory activity and ATP production ability recovered in cells with increased mtDNA levels after removal of the specific siRNA treatment. These experimental results provide direct evidence to substantiate that downregulation of mtDNA copy number and expression may compromise mitochondrial function and subsequent cell growth and morphology. (c) 2007 Wiley-Liss, Inc.

ON THE ELECTRON-TO-NEUTRAL NUMBER DENSITY RATIO IN THE COMA OF COMET 67P/CHURYUMOV–GERASIMENKO: GUIDING EXPRESSION AND SOURCES FOR DEVIATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vigren, E.; Eriksson, A. I.; Edberg, N. J. T.

2015-10-10

We compute partial photoionization frequencies of H{sub 2}O, CO{sub 2}, and CO, the major molecules in the coma of comet 67P/Churyumov–Gerasimenko, the target comet of the ongoing ESA Rosetta mission. Values are computed from Thermosphere Ionosphere Mesosphere Energy and Dynamics/Solar EUV Experiment solar EUV spectra for 2014 August 1, 2015 March 1, and for perihelion (2015 August, as based on prediction). From the varying total photoionization frequency of H{sub 2}O, as computed from 2014 August 1 to 2015 May 20, we derive a simple analytical expression for the electron-to-neutral number density ratio as a function of cometocentric and heliocentric distance. Themore » underlying model assumes radial movement of the coma constituents and does not account for chemical loss or the presence of electric fields. We discuss various effects/processes that can cause deviations between values from the analytical expression and actual electron-to-neutral number density ratios. The analytical expression is thus not strictly meant as predicting the actual electron-to-neutral number density ratio, but is useful in comparisons with observations as an indicator of processes at play in the cometary coma.« less

Linear instability of compound liquid threads in the presence of surfactant

NASA Astrophysics Data System (ADS)

Ye, Han-yu; Yang, Li-jun; Fu, Qing-fei

2017-08-01

This paper investigates the linear instability of compound liquid threads in the presence of surfactant. The limitation of the one-dimensional approximation in previous work [Craster, Matar, and Papageorgiou, Phys. Fluids 15, 3409 (2003), 10.1063/1.1611879] is removed; hence the radial dependence of the axial velocity can be taken into account. Therefore both the stretching and the squeezing modes can be investigated. The disturbance growth rate is reduced with an increase of the dimensionless surface-tension gradient (whether in the stretching or squeezing mode). For the parameter range investigated, it is found that the squeezing mode is much more sensitive to the Marangoni effect than the stretching mode. The disturbance axial velocity and disturbance surfactant concentration for a typical case is investigated. It is found that the disturbance axial velocity is close to uniform in the stretching mode when the dimensionless surface-tension gradient and the wave number are small. In contrast, for wave numbers close to cutoff, or a large dimensionless surface-tension gradient, or in the squeezing mode, the disturbance axial velocity is not uniform. Analytical relations between growth rate and wave number valid in the long-wave limit are derived. In the stretching mode, the flow moves from an extension-dominated regime to a shear-dominated regime when β1+R σ β2 increases through 1 +R σ , where β1 and β2 are the dimensionless surface-tension gradient of the inner and outer interface, respectively, R is the radius ratio, and σ is the surface tension ratio. In the squeezing mode, whatever the values of β1 and β2, the flow is always in the shear-dominated regime. The expressions of the leading-order axial perturbation velocity in the long-wave limit are derived and they explain the applicability of one-dimensional models. It is found that the leading-order axial velocity in the extension-dominated regime is always uniform and one-dimensional models work well in

Alterations in gene expression of proprotein convertases in human lung cancer have a limited number of scenarios.

PubMed

Demidyuk, Ilya V; Shubin, Andrey V; Gasanov, Eugene V; Kurinov, Alexander M; Demkin, Vladimir V; Vinogradova, Tatyana V; Zinovyeva, Marina V; Sass, Alexander V; Zborovskaya, Irina B; Kostrov, Sergey V

2013-01-01

Proprotein convertases (PCs) is a protein family which includes nine highly specific subtilisin-like serine endopeptidases in mammals. The system of PCs is involved in carcinogenesis and levels of PC mRNAs alter in cancer, which suggests expression status of PCs as a possible marker for cancer typing and prognosis. The goal of this work was to assess the information value of expression profiling of PC genes. Quantitative polymerase chain reaction was used for the first time to analyze mRNA levels of all PC genes as well as matrix metalloproteinase genes MMP2 and MMP14, which are substrates of PCs, in 30 matched pairs of samples of human lung cancer tumor and adjacent tissues without pathology. Significant changes in the expression of PCs have been revealed in tumor tissues: increased FURIN mRNA level (p<0.00005) and decreased mRNA levels of PCSK2 (p<0.007), PCSK5 (p<0.0002), PCSK7 (p<0.002), PCSK9 (p<0.00008), and MBTPS1 (p<0.00004) as well as a tendency to increase in the level of PCSK1 mRNA. Four distinct groups of samples have been identified by cluster analysis of the expression patterns of PC genes in tumor vs. normal tissue. Three of these groups covering 80% of samples feature a strong elevation in the expression of a single gene in cancer: FURIN, PCSK1, or PCSK6. Thus, the changes in the expression of PC genes have a limited number of scenarios, which may reflect different pathways of tumor development and cryptic features of tumors. This finding allows to consider the mRNAs of PC genes as potentially important tumor markers.

PHOTOSPHERE EMISSION FROM A HYBRID RELATIVISTIC OUTFLOW WITH ARBITRARY DIMENSIONLESS ENTROPY AND MAGNETIZATION IN GRBs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, He; Zhang, Bing, E-mail: gaohe@physics.unlv.edu, E-mail: zhang@physics.unlv.edu, E-mail: hug18@psu.edu

2015-03-10

In view of the recent Fermi observations of gamma-ray burst (GRB) prompt emission spectra, we develop a theory of photosphere emission of a hybrid relativistic outflow with a hot fireball component (defined by dimensionless entropy η) and a cold Poynting-flux component (defined by magnetization σ{sub 0} at the central engine). We consider the scenarios both without and with sub-photospheric magnetic dissipations. Based on a simplified toy model of jet dynamics, we develop two approaches: a 'bottom-up' approach to predict the temperature (for a non-dissipative photosphere) and luminosity of the photosphere emission and its relative brightness for a given pair ofmore » (η, σ{sub 0}); and a 'top-down' approach to diagnose central engine parameters (η and σ{sub 0}) based on the observed quasi-thermal photosphere emission properties. We show that a variety of observed GRB prompt emission spectra with different degrees of photosphere thermal emission can be reproduced by varying η and σ{sub 0} within the non-dissipative photosphere scenario. In order to reproduce the observed spectra, the outflows of most GRBs need to have a significant σ, both at the central engine and at the photosphere. The σ value at 10{sup 15} cm from the central engine (a possible non-thermal emission site) is usually also greater than unity, so that internal-collision-induced magnetic reconnection and turbulence (ICMART) may be the mechanism to power the non-thermal emission. We apply our top-down approach to GRB 110721A and find that the temporal evolution behavior of its blackbody component can be well interpreted with a time-varying (η, σ{sub 0}) at the central engine, instead of invoking a varying engine base size r {sub 0} as proposed by previous authors.« less

Air pollution in perspective: Health risks of air pollution expressed in equivalent numbers of passively smoked cigarettes.

PubMed

van der Zee, Saskia C; Fischer, Paul H; Hoek, Gerard

2016-07-01

Although the health effects of long term exposure to air pollution are well established, it is difficult to effectively communicate the health risks of this (largely invisible) risk factor to the public and policy makers. The purpose of this study is to develop a method that expresses the health effects of air pollution in an equivalent number of daily passively smoked cigarettes. Defined changes in PM2.5, nitrogen dioxide (NO2) and Black Carbon (BC) concentration were expressed into number of passively smoked cigarettes, based on equivalent health risks for four outcome measures: Low Birth Weight (<2500g at term), decreased lung function (FEV1), cardiovascular mortality and lung cancer. To describe the strength of the relationship with ETS and air pollutants, we summarized the epidemiological literature using published or new meta-analyses. Realistic increments of 10µg/m(3) in PM2.5 and NO2 concentration and a 1µg/m(3) increment in BC concentration correspond to on average (standard error in parentheses) 5.5 (1.6), 2.5 (0.6) and 4.0 (1.2) passively smoked cigarettes per day across the four health endpoints, respectively. The uncertainty reflects differences in equivalence between the health endpoints and uncertainty in the concentration response functions. The health risk of living along a major freeway in Amsterdam is, compared to a counterfactual situation with 'clean' air, equivalent to 10 daily passively smoked cigarettes.. We developed a method that expresses the health risks of air pollution and the health benefits of better air quality in a simple, appealing manner. The method can be used both at the national/regional and the local level. Evaluation of the usefulness of the method as a communication tool is needed. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach

PubMed Central

Shi, Xingjie; Zhao, Qing; Huang, Jian; Xie, Yang; Ma, Shuangge

2015-01-01

Motivation: Both gene expression levels (GEs) and copy number alterations (CNAs) have important biological implications. GEs are partly regulated by CNAs, and much effort has been devoted to understanding their relations. The regulation analysis is challenging with one gene expression possibly regulated by multiple CNAs and one CNA potentially regulating the expressions of multiple genes. The correlations among GEs and among CNAs make the analysis even more complicated. The existing methods have limitations and cannot comprehensively describe the regulation. Results: A sparse double Laplacian shrinkage method is developed. It jointly models the effects of multiple CNAs on multiple GEs. Penalization is adopted to achieve sparsity and identify the regulation relationships. Network adjacency is computed to describe the interconnections among GEs and among CNAs. Two Laplacian shrinkage penalties are imposed to accommodate the network adjacency measures. Simulation shows that the proposed method outperforms the competing alternatives with more accurate marker identification. The Cancer Genome Atlas data are analysed to further demonstrate advantages of the proposed method. Availability and implementation: R code is available at http://works.bepress.com/shuangge/49/ Contact: shuangge.ma@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26342102

32 CFR 1602.19 - Numbers.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 6 2011-07-01 2011-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols. ...

32 CFR 1602.19 - Numbers.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 6 2010-07-01 2010-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols. ...

32 CFR 1602.19 - Numbers.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 6 2012-07-01 2012-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols. ...

32 CFR 1602.19 - Numbers.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 6 2013-07-01 2013-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols. ...

32 CFR 1602.19 - Numbers.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 6 2014-07-01 2014-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols. ...

Numerical study of unsteady MHD oblique stagnation point flow and heat transfer due to an oscillating stream

NASA Astrophysics Data System (ADS)

Javed, T.; Ghaffari, A.; Ahmad, H.

2016-05-01

The unsteady stagnation point flow impinging obliquely on a flat plate in presence of a uniform applied magnetic field due to an oscillating stream has been studied. The governing partial differential equations are transformed into dimensionless form and the stream function is expressed in terms of Hiemenz and tangential components. The dimensionless partial differential equations are solved numerically by using well-known implicit finite difference scheme named as Keller-box method. The obtained results are compared with those available in the literature. It is observed that the results are in excellent agreement with the previous studies. The effects of pertinent parameters involved in the problem namely magnetic parameter, Prandtl number and impinging angle on flow and heat transfer characteristics are illustrated through graphs. It is observed that the influence of magnetic field strength increases the fluid velocity and by the increase of obliqueness parameter, the skin friction increases.

Generalized Knudsen Number for Oscillatory Flows Generated by MEMS and NEMS Resonators

NASA Astrophysics Data System (ADS)

Ekinci, Kamil; Kara, Vural; Yakhot, Victor

2017-11-01

We have explored the scaling behavior of oscillatory flows that are generated by the oscillations of MEMS and NEMS resonators in a gas. If the gas is gradually rarefied, the Navier-Stokes equations begin to fail and a kinetic description of the flow becomes more appropriate. The failure of the Navier-Stokes equations can be thought to take place via two different physical mechanisms: either the continuum hypothesis breaks down as a result of a finite size effect; or local equilibrium is violated due to the high rate of strain. By independently tuning the relevant linear dimensions and the frequencies of the MEMS and NEMS resonators, we experimentally observe these two different physical mechanisms. All the experimental data, however, can be collapsed using a single dimensionless scaling parameter that combines the linear dimension and the frequency of each resonator. This proposed Knudsen number for oscillatory flows is rooted in a fundamental symmetry principle, namely Galilean invariance. We acknowledge support from US NSF through Grant No. CBET-1604075.

Optimum parallel step-sector bearing lubricated with an incompressible fluid

NASA Technical Reports Server (NTRS)

Hamrock, B. J.

1983-01-01

The dimensionless parameters normally associated with a step sector thrust bearing are the film thickness ratio, the dimensionless step location, the number of sectors, the radius ratio, and the angular extent of the lubrication feed groove. The optimum number of sectors and the parallel step configuration for a step sector thrust bearing while considering load capacity or stiffness and assuming an incompressible fluid are presented.

Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hodgson, J. Graeme; Yeh, Ru-Fang; Ray, Amrita

2009-04-03

Development of model systems that recapitulate the molecular heterogeneity observed among glioblastoma multiforme (GBM) tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from the Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7 gain/chromosome-10 loss, a poor-prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBM tumors,more » genomic amplification and overexpression of known GBM oncogenes, such as EGFR, MDM2, CDK6, and MYCN, and novel genes, including NUP107, SLC35E3, MMP1, MMP13, and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M phase, DNA replication, and chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis and cell-cycle module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M progression and/or checkpoint activation. Our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.« less

A dimensionless dynamic contrast enhanced MRI parameter for intra-prostatic tumour target volume delineation: initial comparison with histology

NASA Astrophysics Data System (ADS)

Hrinivich, W. Thomas; Gibson, Eli; Gaed, Mena; Gomez, Jose A.; Moussa, Madeleine; McKenzie, Charles A.; Bauman, Glenn S.; Ward, Aaron D.; Fenster, Aaron; Wong, Eugene

2014-03-01

Purpose: T2 weighted and diffusion weighted magnetic resonance imaging (MRI) show promise in isolating prostate tumours. Dynamic contrast enhanced (DCE)-MRI has also been employed as a component in multi-parametric tumour detection schemes. Model-based parameters such as Ktrans are conventionally used to characterize DCE images and require arterial contrast agent (CR) concentration. A robust parameter map that does not depend on arterial input may be more useful for target volume delineation. We present a dimensionless parameter (Wio) that characterizes CR wash-in and washout rates without requiring arterial CR concentration. Wio is compared to Ktrans in terms of ability to discriminate cancer in the prostate, as demonstrated via comparison with histology. Methods: Three subjects underwent DCE-MRI using gadolinium contrast and 7 s imaging temporal resolution. A pathologist identified cancer on whole-mount histology specimens, and slides were deformably registered to MR images. The ability of Wio maps to discriminate cancer was determined through receiver operating characteristic curve (ROC) analysis. Results: There is a trend that Wio shows greater area under the ROC curve (AUC) than Ktrans with median AUC values of 0.74 and 0.69 respectively, but the difference was not statistically significant based on a Wilcoxon signed-rank test (p = 0.13). Conclusions: Preliminary results indicate that Wio shows potential as a tool for Ktrans QA, showing similar ability to discriminate cancer in the prostate as Ktrans without requiring arterial CR concentration.

Number Guessing

ERIC Educational Resources Information Center

Sezin, Fatin

2009-01-01

It is instructive and interesting to find hidden numbers by using different positional numeration systems. Most of the present guessing techniques use the binary system expressed as less-than, greater-than or present-absent type information. This article describes how, by employing four cards having integers 1-64 written in different colours, one…

Number of X-chromosome genes influences social behavior and vasopressin gene expression in mice

PubMed Central

Cox, Kimberly H.; Quinnies, Kayla M.; Eschendroeder, Alex; Didrick, Paula M.; Eugster, Erica A.; Rissman, Emilie F.

2017-01-01

Summary Sex differences in behavior are widespread and often caused by hormonal differences between the sexes. In addition to hormones, the composition and numbers of the sex chromosomes also affect a variety of sex differences. In humans, X-chromosome genes are implicated in neurobehavioral disorders (i.e. fragile-X, autism). To investigate the role of X-chromosome genes in social behavior, we used a mouse model that has atypical sex chromosome configurations resembling Turner (45, XO) and Klinefelter syndromes (47, XXY). We examined a number of behaviors in juvenile mice. Mice with only one copy of most X-chromosome genes, regardless of gonadal sex, were less social in dyadic interaction and social preference tasks. In the elevated plus maze, mice with one X-chromosome spent less time in the distal ends of the open arms as compared to mice with two copies of X-chromosome genes. Using qRTPCR, we noted that amygdala from female mice with one X-chromosome had higher expression levels of vasopressin (Avp) as compared to mice in the other groups. Finally, in plasma from girls with Turner syndrome we detected reduced vasopressin (AVP) concentrations as compared to control patients. These novel findings link sex chromosome genes with social behavior via concentrations of AVP in brain, adding to our understanding of sex differences in neurobehavioral disorders. PMID:25462900

Transition Heat Transfer Modeling Based on the Characteristics of Turbulent Spots

NASA Technical Reports Server (NTRS)

Simon, Fred; Boyle, Robert

1998-01-01

While turbulence models are being developed which show promise for simulating the transition region on a turbine blade or vane, it is believed that the best approach with the greatest potential for practical use is the use of models which incorporate the physics of turbulent spots present in the transition region. This type of modeling results in the prediction of transition region intermittency which when incorporated in turbulence models give a good to excellent prediction of the transition region heat transfer. Some models are presented which show how turbulent spot characteristics and behavior can be employed to predict the effect of pressure gradient and Mach number on the transition region. The models predict the spot formation rate which is needed, in addition to the transition onset location, in the Narasimha concentrated breakdown intermittency equation. A simplified approach is taken for modeling turbulent spot growth and interaction in the transition region which utilizes the turbulent spot variables governing transition length and spot generation rate. The models are expressed in terms of spot spreading angle, dimensionless spot velocity, dimensionless spot area, disturbance frequency and Mach number. The models are used in conjunction with a computer code to predict the effects of pressure gradient and Mach number on the transition region and compared with VKI experimental turbine data.

Analysis of gene expression in small numbers of purified hemopoietic progenitor cells by RT-PCR.

PubMed

Ziegler, B L; Lamping, C P; Thoma, S J; Fliedner, T M

1995-05-01

Primitive hemopoietic stem cells represent the most probable targets for genetic alterations due to exposure to ionizing irradiation or chemical carcinogens. We have applied a two-step protocol for the purification of CD34+HLA-DR-/low hemopoietic progenitor cells from cord blood (CB). CD34+ cells were isolated by monoclonal antibody (mAb) against CD34 (My10) and immunomagnetic beads. Beads were cleaved off the CD34+ cells by enzymatic treatment with chymopapain. Due to chymopapain-resistance of epitopes recognized by the used mAbs purity control of CD34+ cells and separation into CD34+HLA-DR-/low and CD34+HLA-DR+ subsets could be performed by using flow cytometry. Two miniaturized procedures were applied to isolate poly(A)+ mRNA for the reverse transcription polymerase chain reaction (RT-PCR) from small numbers of CD34+HLA-DR-/low cells. In five experiments, the mean purity of immunomagnetically isolated CD34+ cells was 93.8% +/- 3.9. Flow cytometry sorting of CD34+ cells resulted in pure CD34+HLA-DR-/low populations (purity > 98.8%; range 98.8% to 99.9%; viability > 96%) with an average yield of 2600 +/- 800 cells/5 x 10(7) low density CB cells. By RT-PCR using both poly(A)+ mRNA isolation procedures, sequences corresponding to CD34 and beta 2-microglobulin were amplified from as few as 20 cells. Furthermore, a sequence-independent RT-PCR (SIP-RT-PCR) was applied to amplify the cDNA derived from five erythroblasts isolated from a burst-forming unit-erythroid (BFU-E). Upon hybridization, full-length c-fos message was detected in the SIP-RT-PCR amplified material. Our data demonstrate that gene expression can be detected at the transcriptional level in small numbers of hemopoietic progenitor cells. In addition, the SIP-RT-PCR may allow the amplification of unique mRNA species when subtractive hybridization procedures are performed. The presented data should be useful to analyze gene expression in rare subsets of radiation-exposed immature hemopoietic stem

Acoustic and Seismic Fields of Hydraulic Jumps at Varying Froude Numbers

NASA Astrophysics Data System (ADS)

Ronan, Timothy J.; Lees, Jonathan M.; Mikesell, T. Dylan; Anderson, Jacob F.; Johnson, Jeffrey B.

2017-10-01

Mechanisms that produce seismic and acoustic wavefields near rivers are poorly understood because of a lack of observations relating temporally dependent river conditions to the near-river seismoacoustic fields. This controlled study at the Harry W. Morrison Dam (HWMD) on the Boise River, Idaho, explores how temporal variation in fluvial systems affects surrounding acoustic and seismic fields. Adjusting the configuration of the HWMD changed the river bathymetry and therefore the form of the standing wave below the dam. The HWMD was adjusted to generate four distinct wave regimes that were parameterized through their dimensionless Froude numbers (Fr) and observations of the ambient seismic and acoustic wavefields at the study site. To generate detectable and coherent signals, a standing wave must exceed a threshold Fr value of 1.7, where a nonbreaking undular jump turns into a breaking weak hydraulic jump. Hydrodynamic processes may partially control the spectral content of the seismic and acoustic energies. Furthermore, spectra related to reproducible wave conditions can be used to calibrate and verify fluvial seismic and acoustic models.

Correlation of EGFR expression, gene copy number and clinicopathological status in NSCLC.

PubMed

Gaber, Rania; Watermann, Iris; Kugler, Christian; Reinmuth, Nils; Huber, Rudolf M; Schnabel, Philipp A; Vollmer, Ekkehard; Reck, Martin; Goldmann, Torsten

2014-09-17

Epidermal Growth Factor Receptor (EGFR) targeting therapies are currently of great relevance for the treatment of lung cancer. For this reason, in addition to mutational analysis immunohistochemistry (IHC) of EGFR in lung cancer has been discussed for the decision making of according therapeutic strategies. The aim of this study was to obtain standardization of EGFR-expression methods for the selection of patients who might benefit of EGFR targeting therapies. As a starting point of a broad investigation, aimed at elucidating the expression of EGFR on different biological levels, four EGFR specific antibodies were analyzed concerning potential differences in expression levels by Immunohistochemistry (IHC) and correlated with fluorescence in situ hybridization (FISH) analysis and clinicopathological data. 206 tumor tissues were analyzed in a tissue microarray format employing immunohistochemistry with four different antibodies including Dako PharmDx kit (clone 2-18C9), clone 31G7, clone 2.1E1 and clone SP84 using three different scoring methods. Protein expression was compared to FISH utilizing two different probes. EGFR protein expression determined by IHC with Dako PharmDx kit, clone 31G7 and clone 2.1E1 (p ≤ 0.05) correlated significantly with both FISH probes independently of the three scoring methods; best correlation is shown for 31G7 using the scoring method that defined EGFR positivity when ≥ 10% of the tumor cells show membranous staining of moderate and severe intensity (p=0.001). Overall, our data show differences in EGFR expression determined by IHC, due to the applied antibody. Highest concordance with FISH is shown for antibody clone 31G7, evaluated with score B (p=0.001). On this account, this antibody clone might by utilized for standard evaluation of EGFR expression by IHC. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_165.

Adaptation to acidic soil is achieved by increased numbers of cis-acting elements regulating ALMT1 expression in Holcus lanatus.

PubMed

Chen, Zhi Chang; Yokosho, Kengo; Kashino, Miho; Zhao, Fang-Jie; Yamaji, Naoki; Ma, Jian Feng

2013-10-01

Yorkshire fog (Holcus lanatus), which belongs to the Poaceae family and is a close relative of the agronomic crop oat (Avena sativa), is a widely adaptable grass species that is able to grow on highly acidic soils with high levels of Al, but the mechanism underlying the high Al tolerance is unknown. Here, we characterized two accessions of H. lanatus collected from an acid plot (soil pH 3.6, HL-A) and a neutral plot (pH 7.1, HL-N) in terms of Al tolerance, organic acid anion secretion and related gene expression. In response to Al (pH 4.5), the HL-A roots secreted approximately twice as much malate as the HL-N roots, but there was no difference in citrate secretion. Cloning of the gene HlALMT1 responsible for malate secretion showed that the encoded amino acid sequence did not differ between two accessions, but the expression level in the outer cell layers of the HL-A roots was twice as high as in the HL-N roots. This difference was not due to the genomic copy number, but was due to the number of cis-acting elements for an Al-responsive transcription factor (HlART1) in the promoter region of HlALMT1, as demonstrated by both a yeast one-hybrid assay and a transient assay in tobacco protoplasts. Furthermore, introduction of HlALMT1 driven by the HL-A promoter into rice resulted in significantly more Al-induced malate secretion than introduction of HlALMT1 driven by the HL-N promoter. These findings indicate that the adaptation of H. lanatus to acidic soils may be achieved by increasing number of cis-acting elements for ART1 in the promoter region of the HlALMT1 gene, enhancing the expression of HlALMT1 and the secretion of malate. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Correlations by the entrainment theory of thermodynamic effects for developed cavitation in venturis and comparisons with ogive data

NASA Technical Reports Server (NTRS)

Billet, M. L.; Holl, J. W.; Weir, D. S.

1975-01-01

A semi-empirical entrainment theory was employed to correlate the measured temperature depression, Delta T, in a developed cavity for a venturi. This theory correlates Delta t in terms of the dimensionless numbers of Nusselt, Reynolds, Froude, Weber and Peclet, and dimensionless cavity length, L/D. These correlations are then compared with similar correlations for zero and quarter caliber ogives. In addition, cavitation number data for both limited and developed cavitation in venturis are presented.

Increased progesterone receptor expression in uterine leiomyoma: correlation with age, number of leiomyomas, and clinical symptoms.

PubMed

Tsigkou, Anastasia; Reis, Fernando M; Lee, Meng H; Jiang, Bingjie; Tosti, Claudia; Centini, Gabriele; Shen, Fang-Rong; Chen, You-Guo; Petraglia, Felice

2015-07-01

To investigate the possible correlation between progesterone receptor (PR) expression in uterine leiomyoma or adjacent myometrium and patient's age, size/number of leiomyomas, or clinical symptoms such as dysmenorrhea, acyclic pelvic pain, or menstrual and intermenstrual uterine bleeding. Cross-sectional study. Referral center. Sixty-two Chinese women undergoing elective hysterectomy for uterine leiomyomata. None. Evaluation of PR-total and PR-B mRNA with real-time polymerase chain reaction; PR-A and PR-B proteins quantified by Western blot in leiomyoma tissue and myometrium; symptoms rated by the patients using visual analog scores. The PR-B mRNA and PR-A and PR-B proteins were more concentrated in leiomyomas than in matched myometrium. A direct correlation between PR-B mRNA levels in leiomyoma and age (r = 0.347) and number of tumors (r = 0.295) was found. Conversely, there was an inverse correlation between PR-B mRNA levels in leiomyoma and dysmenorrhea (r = -0.260) and intermenstrual bleeding (r = -0.266). Multiple regression analysis indicated that age (β = 0.363) and the number of myomas (β = 0.296) were independently associated with PR-B mRNA levels in leiomyoma tissue. The levels of PR-B mRNA in leiomyoma tissue are directly associated with the number of tumors and inversely correlated with the intensity of intermenstrual bleeding and dysmenorrhea, suggesting that PR signaling may favor leiomyoma growth while attenuating clinical symptoms. This duality should be taken into account in the clinical management of patients with symptomatic uterine leiomyoma. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

miR-24-2 controls H2AFX expression regardless of gene copy number alteration and induces apoptosis by targeting antiapoptotic gene BCL-2: a potential for therapeutic intervention.

PubMed

Srivastava, Niloo; Manvati, Siddharth; Srivastava, Archita; Pal, Ranjana; Kalaiarasan, Ponnusamy; Chattopadhyay, Shilpi; Gochhait, Sailesh; Dua, Raina; Bamezai, Rameshwar N K

2011-04-04

New levels of gene regulation with microRNA (miR) and gene copy number alterations (CNAs) have been identified as playing a role in various cancers. We have previously reported that sporadic breast cancer tissues exhibit significant alteration in H2AX gene copy number. However, how CNA affects gene expression and what is the role of miR, miR-24-2, known to regulate H2AX expression, in the background of the change in copy number, are not known. Further, many miRs, including miR-24-2, are implicated as playing a role in cell proliferation and apoptosis, but their specific target genes and the pathways contributing to them remain unexplored. Changes in gene copy number and mRNA/miR expression were estimated using real-time polymerase chain reaction assays in two mammalian cell lines, MCF-7 and HeLa, and in a set of sporadic breast cancer tissues. In silico analysis was performed to find the putative target for miR-24-2. MCF-7 cells were transfected with precursor miR-24-2 oligonucleotides, and the gene expression levels of BRCA1, BRCA2, ATM, MDM2, TP53, CHEK2, CYT-C, BCL-2, H2AFX and P21 were examined using TaqMan gene expression assays. Apoptosis was measured by flow cytometric detection using annexin V dye. A luciferase assay was performed to confirm BCL-2 as a valid cellular target of miR-24-2. It was observed that H2AX gene expression was negatively correlated with miR-24-2 expression and not in accordance with the gene copy number status, both in cell lines and in sporadic breast tumor tissues. Further, the cells overexpressing miR-24-2 were observed to be hypersensitive to DNA damaging drugs, undergoing apoptotic cell death, suggesting the potentiating effect of mir-24-2-mediated apoptotic induction in human cancer cell lines treated with anticancer drugs. BCL-2 was identified as a novel cellular target of miR-24-2. mir-24-2 is capable of inducing apoptosis by modulating different apoptotic pathways and targeting BCL-2, an antiapoptotic gene. The study suggests

Heat-Transfer and Pressure Measurements on a Flat-Face Cylinder at a Mach Number Range of 2.49 to 4.44

NASA Technical Reports Server (NTRS)

Burbank, Paige B.; Stallings, Robert L., Jr.

1959-01-01

Heat-transfer coefficients and pressure distributions were obtained on a 4-inch-diameter flat-face cylinder in the Langley Unitary Plan wind tunnel. The measured stagnation heat-transfer coefficient agrees well with 55 percent of the theoretical value predicted by the modified Sibulkin method for a hemisphere. Pressure measurements indicated the dimensionless velocity gradient parameter r du\\ a(sub t) dx, where x=0 at the stagnation point was approximately 0.3 and invariant throughout the Mach number range from 2.49 to 4.44 and the Reynolds number range from 0.77 x 10(exp 6) to 1.46 x 10(exp 6). The heat-transfer coefficients on the cylindrical afterbody could be predicted with reasonable accuracy by flat-plate theory at an angle of attack of 0 deg. At angles of attack the cylindrical afterbody stagnation-line heat transfer could be computed from swept-cylinder theory for large distances back of the nose when the Reynolds number is based on the distance from the flow reattachment points.

Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

NASA Technical Reports Server (NTRS)

Woronowicz, Michael

2017-01-01

Providers of payloads carried aboard the International Space Station must conduct analyses to demonstrate that any planned gaseous venting events generate no more than a certain level of material that may interfere with optical measurements from other experiments or payloads located nearby. This requirement is expressed in terms of a maximum column number density (CND). Depending on the level of rarefaction, such venting may be characterized by effusion for low flow rates, or by a sonic distribution at higher levels. Since the relative locations of other sensitive payloads are often unknown because they may refer to future projects, this requirement becomes a search for the maximum CND along any path.In another application, certain astronomical observations make use of CND to estimate light attenuation from a distant star through gaseous plumes, such as the Fermi Bubbles emanating from the vicinity of the black hole at the center of our Milky Way galaxy, in order to infer the amount of material being expelled via those plumes.This paper presents analytical CND expressions developed for general straight paths based upon a free molecule point source model for steady effusive flow and for a distribution fitted to model flows from a sonic orifice. Among other things, in this Mach number range it is demonstrated that the maximum CND from a distant location occurs along the path parallel to the source plane that intersects the plume axis. For effusive flows this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plumes axis. For sonic plumes this ratio is reduced to about 43.

Effects of Froude number and geometry on water entry of a 2-D ellipse

NASA Astrophysics Data System (ADS)

Zhang, Xu; Liu, Pei-qing; Qu, Qiu-lin; Wang, Rui; Agarwal, Ramesh K.

2018-05-01

By using the finite volume method with volume of fluid model and global dynamic mesh technique, the effects of Froude number and geometry on the water entry process of a 2-D ellipse are investigated numerically. For the time history of the vertical force, the computational fluid dynamics (CFD) results match the experimental data much better than the classical potential-flow theories due to the consideration of the viscosity, turbulence, surface tension, gravity, and compressibility. The results show that the position of peak pressure on ellipse shifts from the spray root to the bottom of ellipse at a critical time. The critical time changes with the geometry and Froude number. By studying the vertical force, the ellipse water entry process can be divided into the initial and late stages based on the critical dimensionless time of about 0.1. The geometry of the ellipse plays a dominant role in the initial stage, while the Froude number is more important in the late stage of entry. The classical Wagner theory is extended to the ellipse water entry, and the predicted maximum value of vertical force coefficient in the initial stage is 4πa/b that matches the CFD results very well, where a and b are the horizontal axis and vertical axis of the ellipse parallel and perpendicular to the initial calm water surface, respectively.

Condensation heat transfer and flow friction in silicon microchannels

NASA Astrophysics Data System (ADS)

Wu, Huiying; Wu, Xinyu; Qu, Jian; Yu, Mengmeng

2008-11-01

An experimental investigation was performed on heat transfer and flow friction characteristics during steam condensation flow in silicon microchannels. Three sets of trapezoidal silicon microchannels, with hydraulic diameters of 77.5 µm, 93.0 µm and 128.5 µm respectively, were tested under different flow and cooling conditions. It was found that both the condensation heat transfer Nusselt number (Nu) and the condensation two-phase frictional multiplier (phi2Lo) were dependent on the steam Reynolds number (Rev), condensation number (Co) and dimensionless hydraulic diameter (Dh/L). With the increase in the steam Reynolds number, condensation number and dimensionless hydraulic diameter, the condensation Nusselt number increased. However, different variations were observed for the condensation two-phase frictional multiplier. With the increase in the steam Reynolds number and dimensionless hydraulic diameter, the condensation two-phase frictional multiplier decreased, while with the increase in the condensation number, the condensation two-phase frictional multiplier increased. Based on the experimental results, dimensionless correlations for condensation heat transfer and flow friction in silicon microchannels were proposed for the first time. These correlations can be used to determine the condensation heat transfer coefficient and pressure drop in silicon microchannels if the steam mass flow rate, cooling rate and geometric parameters are fixed. It was also found that the condensation heat transfer and flow friction have relations to the injection flow (a transition flow pattern from the annular flow to the slug/bubbly flow), and with injection flow moving toward the outlet, both the condensation heat transfer coefficient and the condensation two-phase frictional multiplier increased.

Unsteady MHD blood flow through porous medium in a parallel plate channel

NASA Astrophysics Data System (ADS)

Latha, R.; Rushi Kumar, B.

2017-11-01

In this study, we have analyzed heat and mass transfer effects on unsteady blood flow through parallel plate channel in a saturated porous medium in the presence of a transverse magnetic field with thermal radiation. The governing higher order nonlinear PDE’S are converted to dimensionless equations using dimensionless variables. The dimensionless equations are then solved analytically using boundary conditions by choosing the axial flow transport and the fields of concentration and temperature apart from the normal velocity as a function of y and t. The effects of different pertinent parameters appeared in this model viz thermal radiation, Prandtl number, Heat source parameter, Hartmann number, Permeability parameter, Decay parameter on axial flow transport and the normal velocity are analyzed in detail.

Who can escape the natural number bias in rational number tasks? A study involving students and experts.

PubMed

Obersteiner, Andreas; Hoof, Jo Van; Verschaffel, Lieven; Dooren, Wim Van

2016-08-01

Many learners have difficulties with rational number tasks because they persistently rely on their natural number knowledge, which is not always applicable. Studies show that such a natural number bias can mislead not only children but also educated adults. It is still unclear whether and under what conditions mathematical expertise enables people to be completely unaffected by such a bias on tasks in which people with less expertise are clearly biased. We compared the performance of eighth-grade students and expert mathematicians on the same set of algebraic expression problems that addressed the effect of arithmetic operations (multiplication and division). Using accuracy and response time measures, we found clear evidence for a natural number bias in students but no traces of a bias in experts. The data suggested that whereas students based their answers on their intuitions about natural numbers, expert mathematicians relied on their skilled intuitions about algebraic expressions. We conclude that it is possible for experts to be unaffected by the natural number bias on rational number tasks when they use strategies that do not involve natural numbers. © 2015 The British Psychological Society.

Expression of c-Fos in the rat retrosplenial cortex during instrumental re-learning of appetitive bar-pressing depends on the number of stages of previous training.

PubMed

Svarnik, Olga E; Bulava, Alexandra I; Alexandrov, Yuri I

2013-01-01

Learning is known to be accompanied by induction of c-Fos expression in cortical neurons. However, not all neurons are involved in this process. What the c-Fos expression pattern depends on is still unknown. In the present work we studied whether and to what degree previous animal experience about Task 1 (the first phase of an instrumental learning) influenced neuronal c-Fos expression in the retrosplenial cortex during acquisition of Task 2 (the second phase of an instrumental learning). Animals were progressively shaped across days to bar-press for food at the left side of the experimental chamber (Task 1). This appetitive bar-pressing behavior was shaped by nine stages ("9 stages" group), five stages ("5 stages" group) or one intermediate stage ("1 stage" group). After all animals acquired the first skill and practiced it for five days, the bar and feeder on the left, familiar side of the chamber were inactivated, and the animals were allowed to learn a similar instrumental task at the opposite side of the chamber using another pair of a bar and a feeder (Task 2). The highest number of c-Fos positive neurons was found in the retrosplenial cortex of "1 stage" animals as compared to the other groups. The number of c-Fos positive neurons in "5 stages" group animals was significantly lower than in "1 stage" animals and significantly higher than in "9 stages" animals. The number of c-Fos positive neurons in the cortex of "9 stages" animals was significantly higher than in home caged control animals. At the same time, there were no significant differences between groups in such behavioral variables as the number of entrees into the feeder or bar zones during Task 2 learning. Our results suggest that c-Fos expression in the retrosplenial cortex during Task 2 acquisition was influenced by the previous learning history.

Substrate mass transfer: analytical approach for immobilized enzyme reactions

NASA Astrophysics Data System (ADS)

Senthamarai, R.; Saibavani, T. N.

2018-04-01

In this paper, the boundary value problem in immobilized enzyme reactions is formulated and approximate expression for substrate concentration without external mass transfer resistance is presented. He’s variational iteration method is used to give approximate and analytical solutions of non-linear differential equation containing a non linear term related to enzymatic reaction. The relevant analytical solution for the dimensionless substrate concentration profile is discussed in terms of dimensionless reaction parameters α and β.

The effect of visitor number and spice provisioning in pacing expression by jaguars evaluated through a case study.

PubMed

Vidal, L S; Guilherme, F R; Silva, V F; Faccio, M C S R; Martins, M M; Briani, D C

2016-06-01

Captive animals exhibit stereotypic pacing in response to multiple causes, including the inability to escape from human contact. Environmental enrichment techniques can minimize pacing expression. By using an individual-based approach, we addressed whether the amount of time two males and a female jaguar (Panthera onca) devote to pacing varied with the number of visitors and tested the effectiveness of cinnamon and black pepper in reducing pacing. The amount of time that all jaguars engaged in pacing increased significantly with the number of visitors. Despite the difference between the males regarding age and housing conditions, both devoted significantly less time to pacing following the addition of both spices, which indicates their suitability as enrichment techniques. Mean time devoted to pacing among the treatments did not differ for the female. Our findings pointed out to the validity of individual-based approaches, as they can reveal how suitable olfactory stimuli are to minimizing stereotypies irrespective of particular traits.

Theory of linear sweep voltammetry with diffuse charge: Unsupported electrolytes, thin films, and leaky membranes

NASA Astrophysics Data System (ADS)

Yan, David; Bazant, Martin Z.; Biesheuvel, P. M.; Pugh, Mary C.; Dawson, Francis P.

2017-03-01

Linear sweep and cyclic voltammetry techniques are important tools for electrochemists and have a variety of applications in engineering. Voltammetry has classically been treated with the Randles-Sevcik equation, which assumes an electroneutral supported electrolyte. In this paper, we provide a comprehensive mathematical theory of voltammetry in electrochemical cells with unsupported electrolytes and for other situations where diffuse charge effects play a role, and present analytical and simulated solutions of the time-dependent Poisson-Nernst-Planck equations with generalized Frumkin-Butler-Volmer boundary conditions for a 1:1 electrolyte and a simple reaction. Using these solutions, we construct theoretical and simulated current-voltage curves for liquid and solid thin films, membranes with fixed background charge, and cells with blocking electrodes. The full range of dimensionless parameters is considered, including the dimensionless Debye screening length (scaled to the electrode separation), Damkohler number (ratio of characteristic diffusion and reaction times), and dimensionless sweep rate (scaled to the thermal voltage per diffusion time). The analysis focuses on the coupling of Faradaic reactions and diffuse charge dynamics, although capacitive charging of the electrical double layers is also studied, for early time transients at reactive electrodes and for nonreactive blocking electrodes. Our work highlights cases where diffuse charge effects are important in the context of voltammetry, and illustrates which regimes can be approximated using simple analytical expressions and which require more careful consideration.

Granular-flow rheology: Role of shear-rate number in transition regime

USGS Publications Warehouse

Chen, C.-L.; Ling, C.-H.

1996-01-01

This paper examines the rationale behind the semiempirical formulation of a generalized viscoplastic fluid (GVF) model in the light of the Reiner-Rivlin constitutive theory and the viscoplastic theory, thereby identifying the parameters that control the rheology of granular flow. The shear-rate number (N) proves to be among the most significant parameters identified from the GVF model. As N ??? 0 and N ??? ???, the GVF model can reduce asymptotically to the theoretical stress versus shear-rate relations in the macroviscous and graininertia regimes, respectively, where the grain concentration (C) also plays a major role in the rheology of granular flow. Using available data obtained from the rotating-cylinder experiments of neutrally buoyant solid spheres dispersing in an interstitial fluid, the shear stress for granular flow in transition between the two regimes proves dependent on N and C in addition to some material constants, such as the coefficient of restitution. The insufficiency of data on rotating-cylinder experiments cannot presently allow the GVF model to predict how a granular flow may behave in the entire range of N; however, the analyzed data provide an insight on the interrelation among the relevant dimensionless parameters.

Exact analysis of surface field reduction due to field-emitted vacuum space charge, in parallel-plane geometry, using simple dimensionless equations

NASA Astrophysics Data System (ADS)

Forbes, Richard G.

2008-10-01

This paper reports (a) a simple dimensionless equation relating to field-emitted vacuum space charge (FEVSC) in parallel-plane geometry, namely 9ζ2θ2-3θ-4ζ+3=0, where ζ is the FEVSC "strength" and θ is the reduction in emitter surface field (θ =field-with/field-without FEVSC), and (b) the formula j =9θ2ζ/4, where j is the ratio of emitted current density JP to that predicted by Child's law. These equations apply to any charged particle, positive or negative, emitted with near-zero kinetic energy. They yield existing and additional basic formulas in planar FEVSC theory. The first equation also yields the well-known cubic equation describing the relationship between JP and applied voltage; a method of analytical solution is described. Illustrative FEVSC effects in a liquid metal ion source and in field electron emission are discussed. For Fowler-Nordheim plots, a "turn-over" effect is predicted in the high FEVSC limit. The higher the voltage-to-local-field conversion factor for the emitter concerned, then the higher is the field at which turn over occurs. Past experiments have not found complete turn over; possible reasons are noted. For real field emitters, planar theory is a worst-case limit; however, adjusting ζ on the basis of Monte Carlo calculations might yield formulae adequate for real situations.

Radiation effects on the mixed convection flow induced by an inclined stretching cylinder with non-uniform heat source/sink.

PubMed

Hayat, Tasawar; Qayyum, Sajid; Alsaedi, Ahmed; Asghar, Saleem

2017-01-01

This study investigates the mixed convection flow of Jeffrey liquid by an impermeable inclined stretching cylinder. Thermal radiation and non-uniform heat source/sink are considered. The convective boundary conditions at surface are imposed. Nonlinear expressions of momentum, energy and concentration are transformed into dimensionless systems. Convergent homotopic solutions of the governing systems are worked out by employing homotopic procedure. Impact of physical variables on the velocity, temperature and concentration distributions are sketched and discussed. Numerical computations for skin friction coefficient, local Nusselt and Sherwood numbers are carried out. It is concluded that velocity field enhances for Deborah number while reverse situation is observed regarding ratio of relaxation to retardation times. Temperature and heat transfer rate are enhanced via larger thermal Biot number. Effect of Schmidt number on the concentration and local Sherwood number is quite reverse.

Radiation effects on the mixed convection flow induced by an inclined stretching cylinder with non-uniform heat source/sink

PubMed Central

Hayat, Tasawar; Qayyum, Sajid; Alsaedi, Ahmed; Asghar, Saleem

2017-01-01

This study investigates the mixed convection flow of Jeffrey liquid by an impermeable inclined stretching cylinder. Thermal radiation and non-uniform heat source/sink are considered. The convective boundary conditions at surface are imposed. Nonlinear expressions of momentum, energy and concentration are transformed into dimensionless systems. Convergent homotopic solutions of the governing systems are worked out by employing homotopic procedure. Impact of physical variables on the velocity, temperature and concentration distributions are sketched and discussed. Numerical computations for skin friction coefficient, local Nusselt and Sherwood numbers are carried out. It is concluded that velocity field enhances for Deborah number while reverse situation is observed regarding ratio of relaxation to retardation times. Temperature and heat transfer rate are enhanced via larger thermal Biot number. Effect of Schmidt number on the concentration and local Sherwood number is quite reverse. PMID:28441392

Analysis of activation energy in Couette-Poiseuille flow of nanofluid in the presence of chemical reaction and convective boundary conditions

NASA Astrophysics Data System (ADS)

Zeeshan, A.; Shehzad, N.; Ellahi, R.

2018-03-01

The motivation of the current article is to explore the energy activation in MHD radiative Couette-Poiseuille flow nanofluid in horizontal channel with convective boundary conditions. The mathematical model of Buongiorno [1] effectively describes the current flow analysis. Additionally, the impact of chemical reaction is also taken in account. The governing flow equations are simplified with the help of boundary layer approximations. Non-linear coupled equations for momentum, energy and mass transfer are tackled with analytical (HAM) technique. The influence of dimensionless convergence parameter like Brownian motion parameter, radiation parameter, buoyancy ratio parameter, dimensionless activation energy, thermophoresis parameter, temperature difference parameter, dimensionless reaction rate, Schmidt number, Brinkman number, Biot number and convection diffusion parameter on velocity, temperature and concentration profiles are discussed graphically and in tabular form. From the results, it is elaborate that the nanoparticle concentration is directly proportional to the chemical reaction with activation energy and the performance of Brownian motion on nanoparticle concentration gives reverse pattern to that of thermophoresis parameter.

Expression of c-Fos in the rat retrosplenial cortex during instrumental re-learning of appetitive bar-pressing depends on the number of stages of previous training

PubMed Central

Svarnik, Olga E.; Bulava, Alexandra I.; Alexandrov, Yuri I.

2013-01-01

Learning is known to be accompanied by induction of c-Fos expression in cortical neurons. However, not all neurons are involved in this process. What the c-Fos expression pattern depends on is still unknown. In the present work we studied whether and to what degree previous animal experience about Task 1 (the first phase of an instrumental learning) influenced neuronal c-Fos expression in the retrosplenial cortex during acquisition of Task 2 (the second phase of an instrumental learning). Animals were progressively shaped across days to bar-press for food at the left side of the experimental chamber (Task 1). This appetitive bar-pressing behavior was shaped by nine stages (“9 stages” group), five stages (“5 stages” group) or one intermediate stage (“1 stage” group). After all animals acquired the first skill and practiced it for five days, the bar and feeder on the left, familiar side of the chamber were inactivated, and the animals were allowed to learn a similar instrumental task at the opposite side of the chamber using another pair of a bar and a feeder (Task 2). The highest number of c-Fos positive neurons was found in the retrosplenial cortex of “1 stage” animals as compared to the other groups. The number of c-Fos positive neurons in “5 stages” group animals was significantly lower than in “1 stage” animals and significantly higher than in “9 stages” animals. The number of c-Fos positive neurons in the cortex of “9 stages” animals was significantly higher than in home caged control animals. At the same time, there were no significant differences between groups in such behavioral variables as the number of entrees into the feeder or bar zones during Task 2 learning. Our results suggest that c-Fos expression in the retrosplenial cortex during Task 2 acquisition was influenced by the previous learning history. PMID:23847484

Near-wall effects for momentum, heat and mass transport in gas-particle suspensions at moderate Reynolds numbers

NASA Astrophysics Data System (ADS)

Radl, Stefan; Municchi, Federico; Goniva, Christoph

2016-11-01

Understanding transport phenomena in fluid-particle systems is of primary importance for the design of large-scale equipment, e.g., in the chemical industry. Typically, the analysis of such systems is performed by numerically solving a set of partial differential equations modeling the particle phase and the fluid phase as interpenetrating continua. Such models require a number of closure models that are often constructed via spatial filtering of data obtained from particle-resolved direct numerical simulations (PR-DNS). In the present work we make use of PR-DNS to evaluate corrections to existing closure models. Specifically, we aim on accounting for wall effects on the fluid-particle drag force and the particle-individual Nusselt number. We then propose an improved closure model to be used in particle-unresolved Euler-Lagrange (PU-EL) simulations. We demonstrate that such an advanced closure should account for a dimensionless filter size, as well as a normalized distance from the wall. In addition, we make an attempt to model the filtered fluid velocity profile in wall-bounded suspension flows. The authors acknowledge funding from the European Commission through FP7 Grant Agreement No. 604656, as well as VSC-3 and dcluster.tugraz.at.

A support vector regression-firefly algorithm-based model for limiting velocity prediction in sewer pipes.

PubMed

Ebtehaj, Isa; Bonakdari, Hossein

2016-01-01

Sediment transport without deposition is an essential consideration in the optimum design of sewer pipes. In this study, a novel method based on a combination of support vector regression (SVR) and the firefly algorithm (FFA) is proposed to predict the minimum velocity required to avoid sediment settling in pipe channels, which is expressed as the densimetric Froude number (Fr). The efficiency of support vector machine (SVM) models depends on the suitable selection of SVM parameters. In this particular study, FFA is used by determining these SVM parameters. The actual effective parameters on Fr calculation are generally identified by employing dimensional analysis. The different dimensionless variables along with the models are introduced. The best performance is attributed to the model that employs the sediment volumetric concentration (C(V)), ratio of relative median diameter of particles to hydraulic radius (d/R), dimensionless particle number (D(gr)) and overall sediment friction factor (λ(s)) parameters to estimate Fr. The performance of the SVR-FFA model is compared with genetic programming, artificial neural network and existing regression-based equations. The results indicate the superior performance of SVR-FFA (mean absolute percentage error = 2.123%; root mean square error =0.116) compared with other methods.

The quantitation of buffering action I. A formal & general approach.

PubMed

Schmitt, Bernhard M

2005-03-15

Although "buffering" as a homeostatic mechanism is a universal phenomenon, the quantitation of buffering action remains controversial and problematic. Major shortcomings are: lack of a buffering strength unit for some buffering phenomena, multiple and mutually incommensurable units for others, and lack of a genuine ratio scale for buffering strength. Here, I present a concept of buffering that overcomes these shortcomings. Briefly, when, for instance, some "free" H+ ions are added to a solution (e.g. in the form of strong acid), buffering is said to be present when not all H+ ions remain "free" (i.e., bound to H2O), but some become "bound" (i.e., bound to molecules other than H2O). The greater the number of H+ ions that become "bound" in this process, the greater the buffering action. This number can be expressed in two ways: 1) With respect to the number of total free ions added as "buffering coefficient b", defined in differential form as b = d(bound)/d(total). This measure expresses buffering action from nil to complete by a dimensionless number between 0 and 1, analogous to probabilites. 2) With respect to the complementary number of added ions that remain free as "buffering ratio B", defined as the differential B = d(bound)/d(free). The buffering ratio B provides an absolute ratio scale, where buffering action from nil to perfect corresponds to dimensionless numbers between 0 and infinity, and where equal differences of buffering action result in equal intervals on the scale. Formulated in purely mathematical, axiomatic form, the concept reveals striking overlap with the mathematical concept of probability. However, the concept also allows one to devise simple physical models capable of visualizing buffered systems and their behavior in an exact yet intuitive way. These two measures of buffering action can be generalized easily to any arbitrary quantity that partitions into two compartments or states, and are thus suited to serve as standard units for

Rebuttal to "On the distribution of the modulus of Gabor wavelet coefficients and the upper bound of the dimensionless smoothness index in the case of additive Gaussian noises: Revisited" by Dong Wang, Qiang Zhou, and Kwok-Leung Tsui

NASA Astrophysics Data System (ADS)

Soltani Bozchalooi, Iman; Liang, Ming

2018-04-01

A discussion paper entitled "On the distribution of the modulus of Gabor wavelet coefficients and the upper bound of the dimensionless smoothness index in the case of additive Gaussian noises: revisited" by Dong Wang, Qiang Zhou, Kwok-Leung Tsui has been brought to our attention recently. This discussion paper (hereafter called Wang et al. paper) is based on arguments that are fundamentally incorrect and which we rebut within this commentary. However, as the flaws in the arguments proposed by Wang et al. are clear, we will keep this rebuttal as brief as possible.

A retrospective analysis of RET translocation, gene copy number gain and expression in NSCLC patients treated with vandetanib in four randomized Phase III studies.

PubMed

Platt, Adam; Morten, John; Ji, Qunsheng; Elvin, Paul; Womack, Chris; Su, Xinying; Donald, Emma; Gray, Neil; Read, Jessica; Bigley, Graham; Blockley, Laura; Cresswell, Carl; Dale, Angela; Davies, Amanda; Zhang, Tianwei; Fan, Shuqiong; Fu, Haihua; Gladwin, Amanda; Harrod, Grace; Stevens, James; Williams, Victoria; Ye, Qingqing; Zheng, Li; de Boer, Richard; Herbst, Roy S; Lee, Jin-Soo; Vasselli, James

2015-03-23

To determine the prevalence of RET rearrangement genes, RET copy number gains and expression in tumor samples from four Phase III non-small-cell lung cancer (NSCLC) trials of vandetanib, a selective inhibitor of VEGFR, RET and EGFR signaling, and to determine any association with outcome to vandetanib treatment. Archival tumor samples from the ZODIAC ( NCT00312377 , vandetanib ± docetaxel), ZEAL ( NCT00418886 , vandetanib ± pemetrexed), ZEPHYR ( NCT00404924 , vandetanib vs placebo) and ZEST ( NCT00364351 , vandetanib vs erlotinib) studies were evaluated by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) in 944 and 1102 patients. The prevalence of RET rearrangements by FISH was 0.7% (95% CI 0.3-1.5%) among patients with a known result. Seven tumor samples were positive for RET rearrangements (vandetanib, n = 3; comparator, n = 4). 2.8% (n = 26) of samples had RET amplification (innumerable RET clusters, or ≥7 copies in > 10% of tumor cells), 8.1% (n = 76) had low RET gene copy number gain (4-6 copies in ≥40% of tumor cells) and 8.3% (n = 92) were RET expression positive (signal intensity ++ or +++ in >10% of tumor cells). Of RET-rearrangement-positive patients, none had an objective response in the vandetanib arm and one patient responded in the comparator arm. Radiologic evidence of tumor shrinkage was observed in two patients treated with vandetanib and one treated with comparator drug. The objective response rate was similar in the vandetanib and comparator arms for patients positive for RET copy number gains or RET protein expression. We have identified prevalence for three RET biomarkers in a population predominated by non-Asians and smokers. RET rearrangement prevalence was lower than previously reported. We found no evidence of a differential benefit for efficacy by IHC and RET gene copy number gains. The low prevalence of RET rearrangements (0.7%) prevents firm conclusions regarding association of vandetanib treatment with

Breast cancer cell cyclooxygenase-2 expression alters extracellular matrix structure and function and numbers of cancer associated fibroblasts.

PubMed

Krishnamachary, Balaji; Stasinopoulos, Ioannis; Kakkad, Samata; Penet, Marie-France; Jacob, Desmond; Wildes, Flonne; Mironchik, Yelena; Pathak, Arvind P; Solaiyappan, Meiyappan; Bhujwalla, Zaver M

2017-03-14

Cyclooxygenase-2 (COX-2) is a critically important mediator of inflammation that significantly influences tumor angiogenesis, invasion, and metastasis. We investigated the role of COX-2 expressed by triple negative breast cancer cells in altering the structure and function of the extracellular matrix (ECM). COX-2 downregulation effects on ECM structure and function were investigated using magnetic resonance imaging (MRI) and second harmonic generation (SHG) microscopy of tumors derived from triple negative MDA-MB-231 breast cancer cells, and a derived clone stably expressing a short hairpin (shRNA) molecule downregulating COX-2. MRI of albumin-GdDTPA was used to characterize macromolecular fluid transport in vivo and SHG microscopy was used to quantify collagen 1 (Col1) fiber morphology. COX-2 downregulation decreased Col1 fiber density and altered macromolecular fluid transport. Immunohistochemistry identified significantly fewer activated cancer associated fibroblasts (CAFs) in low COX-2 expressing tumors. Metastatic lung nodules established by COX-2 downregulated cells were infrequent, smaller, and contained fewer Col1 fibers.COX-2 overexpression studies were performed with tumors derived from triple negative SUM-149 breast cancer cells lentivirally transduced to overexpress COX-2. SHG microscopy identified significantly higher Col1 fiber density in COX-2 overexpressing tumors with an increase of CAFs. These data expand upon the roles of COX-2 in shaping the structure and function of the ECM in primary and metastatic tumors, and identify the potential role of COX-2 in modifying the number of CAFs in tumors that may have contributed to the altered ECM.

77 FR 40527 - New Express Mail Price Category-Express Mail Padded Flat Rate Envelope

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-10

... POSTAL SERVICE 39 CFR Part 111 New Express Mail Price Category--Express Mail Padded Flat Rate.... SUPPLEMENTARY INFORMATION: This final rule describes a new price category under Express Mail, Express Mail... new price category is available under Docket Number CP2012-39 on the Postal Regulatory Commission's...

Lake Number, a quantitative indicator of mixing used to estimate changes in dissolved oxygen

USGS Publications Warehouse

Robertson, Dale M.; Imberger, Jorg

1994-01-01

Lake Number, LN, values are shown to be quantitative indicators of deep mixing in lakes and reservoirs that can be used to estimate changes in deep water dissolved oxygen (DO) concentrations. LN is a dimensionless parameter defined as the ratio of the moments about the center of volume of the water body, of the stabilizing force of gravity associated with density stratification to the destabilizing forces supplied by wind, cooling, inflow, outflow, and other artificial mixing devices. To demonstrate the universality of this parameter, LN values are used to describe the extent of deep mixing and are compared with changes in DO concentrations in three reservoirs in Australia and four lakes in the U.S.A., which vary in productivity and mixing regimes. A simple model is developed which relates changes in LN values, i.e., the extent of mixing, to changes in near bottom DO concentrations. After calibrating the model for a specific system, it is possible to use real-time LN values, calculated using water temperature profiles and surface wind velocities, to estimate changes in DO concentrations (assuming unchanged trophic conditions).

Stagnation Region Heat Transfer: The Influence of Turbulence Parameters, Reynolds Number and Body Shape

NASA Technical Reports Server (NTRS)

Vanfossen, G. James; Simoneau, Robert J.

1994-01-01

The effect of velocity gradient on stagnation region heat transfer augmentation by free stream turbulence was investigated. Heat transfer was measured in the stagnation region of four models with elliptical leading edges with ratios of major to minor axes of 1:1, 1.5:1, 2.25:1, and 3:1. Four geometrically similar, square bar, square mesh, biplane grids were used to generate free stream turbulence with different intensities and length. Heat transfer measurements were made for the following ranges of parameters: Reynolds number, based on leading edge diameter, 37,000 to 228,000; dimensionless leading edge velocity gradient, 1.20 to 1.80; turbulence intensity, 1.1 to 15.9%; and length scale to leading edge diameter ratio, 0.05 to 0.30. Stagnation point heat transfer augmentation by free stream turbulence can be predicted using a modified version of a previously developed correlation for a circular leading edge. Heat transfer augmentation was independent of body shape at the stagnation point. The heat transfer distribution down-stream from the stagnation point can be predicted using the normalized laminar heat transfer distribution.

Gas density effect on dropsize of simulated fuel sprays

NASA Technical Reports Server (NTRS)

Ingebo, Robert D.

1989-01-01

Two-phase flow in pneumatic two-fluid fuel nozzles was investigated experimentally to determine the effect of atomizing-gas density and gas mass-flux on liquid-jet breakup in sonic-velocity gas-flow. Dropsize data were obtained for the following atomizing-gases: nitrogen; argon; carbon dioxide; and helium. They were selected to cover a gas molecular-weight range of 4 to 44. Atomizing-gas mass-flux ranged from 6 to 50 g/sq cm-sec and four differently sized two-fluid fuel nozzles were used having orifice diameters that varied from 0.32 to 0.56 cm. The ratio of liquid-jet diameter to SMD, D sub o/D sub 32, was correlated with aerodynamic and liquid-surface forces based on the product of the Weber and Reynolds number, We*Re, and gas-to-liquid density ratio, rho sub g/rho sub l. To correlate spray dropsize with breakup forces produced by using different atomizing-gases, a new molecular-scale dimensionless group was derived. The derived dimensionless group was used to obtain an expression for the ratio of liquid-jet diameter to SMD, D sub o/D sub 32. The mathematical expression of this phenomenon incorporates the product of the Weber and Reynolds number, liquid viscosity, surface tension, acoustic gas velocity, the RMS velocity of gas molecules, the acceleration of gas molecules due to gravity, and gas viscosity. The mathematical expression encompassing these parameters agrees well with the atomization theory for liquid-jet breakup in high velocity gas flow. Also, it was found that at the same gas mass-flux, helium was considerably more effective than nitrogen in producing small droplet sprays with SMD's in the order of 5 micrometers.

Hacking DNA copy number for circuit engineering.

PubMed

Wu, Feilun; You, Lingchong

2017-07-27

DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

How fundamental are fundamental constants?

NASA Astrophysics Data System (ADS)

Duff, M. J.

2015-01-01

I argue that the laws of physics should be independent of one's choice of units or measuring apparatus. This is the case if they are framed in terms of dimensionless numbers such as the fine structure constant, ?. For example, the standard model of particle physics has 19 such dimensionless parameters whose values all observers can agree on, irrespective of what clock, rulers or scales? they use to measure them. Dimensional constants, on the other hand, such as ?, c, G, e and k ?, are merely human constructs whose number and values differ from one choice of units to the next. In this sense, only dimensionless constants are 'fundamental'. Similarly, the possible time variation of dimensionless fundamental 'constants' of nature is operationally well defined and a legitimate subject of physical enquiry. By contrast, the time variation of dimensional constants such as ? or ? on which a good many (in my opinion, confusing) papers have been written, is a unit-dependent phenomenon on which different observers might disagree depending on their apparatus. All these confusions disappear if one asks only unit-independent questions. We provide a selection of opposing opinions in the literature and respond accordingly.

Increased numbers of preexisting memory CD8 T cells and decreased T-bet expression can restrain terminal differentiation of secondary effector and memory CD8 T cells.

PubMed

Joshi, Nikhil S; Cui, Weiguo; Dominguez, Claudia X; Chen, Jonathan H; Hand, Timothy W; Kaech, Susan M

2011-10-15

Memory CD8 T cells acquire effector memory cell properties after reinfection and may reach terminally differentiated, senescent states ("Hayflick limit") after multiple infections. The signals controlling this process are not well understood, but we found that the degree of secondary effector and memory CD8 T cell differentiation was intimately linked to the amount of T-bet expressed upon reactivation and preexisting memory CD8 T cell number (i.e., primary memory CD8 T cell precursor frequency) present during secondary infection. Compared with naive cells, memory CD8 T cells were predisposed toward terminal effector (TE) cell differentiation because they could immediately respond to IL-12 and induce T-bet, even in the absence of Ag. TE cell formation after secondary (2°) or tertiary infections was dependent on increased T-bet expression because T-bet(+/-) cells were resistant to these phenotypic changes. Larger numbers of preexisting memory CD8 T cells limited the duration of 2° infection and the amount of IL-12 produced, and consequently, this reduced T-bet expression and the proportion of 2° TE CD8 T cells that formed. Together, these data show that over repeated infections, memory CD8 T cell quality and proliferative fitness is not strictly determined by the number of serial encounters with Ag or cell divisions, but is a function of the CD8 T cell differentiation state, which is genetically controlled in a T-bet-dependent manner. This differentiation state can be modulated by preexisting memory CD8 T cell number and the intensity of inflammation during reinfection. These results have important implications for vaccinations involving prime-boost strategies.

Viscous decay of nonlinear oscillations of a spherical bubble at large Reynolds number

NASA Astrophysics Data System (ADS)

Smith, W. R.; Wang, Q. X.

2017-08-01

The long-time viscous decay of large-amplitude bubble oscillations is considered in an incompressible Newtonian fluid, based on the Rayleigh-Plesset equation. At large Reynolds numbers, this is a multi-scaled problem with a short time scale associated with inertial oscillation and a long time scale associated with viscous damping. A multi-scaled perturbation method is thus employed to solve the problem. The leading-order analytical solution of the bubble radius history is obtained to the Rayleigh-Plesset equation in a closed form including both viscous and surface tension effects. Some important formulae are derived including the following: the average energy loss rate of the bubble system during each cycle of oscillation, an explicit formula for the dependence of the oscillation frequency on the energy, and an implicit formula for the amplitude envelope of the bubble radius as a function of the energy. Our theory shows that the energy of the bubble system and the frequency of oscillation do not change on the inertial time scale at leading order, the energy loss rate on the long viscous time scale being inversely proportional to the Reynolds number. These asymptotic predictions remain valid during each cycle of oscillation whether or not compressibility effects are significant. A systematic parametric analysis is carried out using the above formula for the energy of the bubble system, frequency of oscillation, and minimum/maximum bubble radii in terms of the Reynolds number, the dimensionless initial pressure of the bubble gases, and the Weber number. Our results show that the frequency and the decay rate have substantial variations over the lifetime of a decaying oscillation. The results also reveal that large-amplitude bubble oscillations are very sensitive to small changes in the initial conditions through large changes in the phase shift.

Functional effects of CCL3L1 copy number

PubMed Central

Carpenter, Danielle; McIntosh, Richard S; Pleass, Richard J; Armour, John AL

2012-01-01

Copy number variation (CNV) is becoming increasingly important as a feature of human variation in disease susceptibility studies. However, the consequences of copy number variation are not so well understood. Here we present data exploring the functional consequences of copy number variation of CCL3L1 in 55 independent UK samples with no known clinical phenotypes. Copy number of CCL3L1 was determined by the paralogue ratio test (PRT), and expression levels of MIP-1α and mRNA from stimulated monocytes were measured and analysed. The data show no statistically significant association of MIP-1α protein levels with copy number. However, there was a significant correlation between copy number and CCL3L1:CCL3 mRNA ratio. The data also provide evidence that expression of CCL3 predominates in both protein and mRNA, and therefore the observed variation of CCL3 is potentially more important biologically than that of copy number variation of CCL3L1. PMID:22476153

Development of thermal stratification and destratification scaling concepts. Volume 1: Definition of thermal stratification scaling parameters and experimental investigations

NASA Technical Reports Server (NTRS)

Lovrich, T. N.; Schwartz, S. H.

1975-01-01

The dimensionless parameters associated with the thermal stratification and pressure history of a heated container of liquid and its vapor were examined. The Modified Grashof number, the Fourier number, and an Interface number were parameterized using a single test liquid, Freon 113. Cylindrical test tanks with spherical dome end caps were built. Blanket heaters covered the tanks and thermocouples monitored the temperatures of the liquid, the ullage, the tank walls, and the foam insulation encapsulating the tank. A centrifuge was used for the 6 inch tank to preserve the same scaling parameter values between it and the larger tanks. Tests were conducted over a range of Gr* values and the degree of scaling was checked by comparing the dimensionless pressures and temperatures for each scaled pair of tests. Results indicate that the bulk liquid temperature, the surface temperature of the liquid, and the tank pressure can be scaled with the three dimensionless parameters. Some deviation was, however, found in the detailed temperature profiles between the scaled pairs of tests.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

Epstein-Barr Virus DNA Enhances Diptericin Expression and Increases Hemocyte Numbers in Drosophila melanogaster via the Immune Deficiency Pathway.

PubMed

Sherri, Nour; Salloum, Noor; Mouawad, Carine; Haidar-Ahmad, Nathaline; Shirinian, Margret; Rahal, Elias A

2018-01-01

Infection with the Epstein-Barr virus (EBV) is associated with several malignancies and autoimmune diseases in humans. The following EBV infection and establishment of latency, recurrences frequently occur resulting in potential viral DNA shedding, which may then trigger the activation of immune pathways. We have previously demonstrated that levels of the pro-inflammatory cytokine IL-17, which is associated with several autoimmune diseases, are increased in response to EBV DNA injection in mice. Whether other pro-inflammatory pathways are induced in EBV DNA pathobiology remains to be investigated. The complexity of mammalian immune systems presents a challenge to studying differential activities of their intricate immune pathways in response to a particular immune stimulus. In this study, we used Drosophila melanogaster to identify innate humoral and cellular immune pathways that are activated in response to EBV DNA. Injection of wild-type adult flies with EBV DNA induced the immune deficiency (IMD) pathway resulting in enhanced expression of the antimicrobial peptide diptericin. Furthermore, EBV DNA increased the number of hemocytes in flies. Conditional silencing of the IMD pathway decreased diptericin expression in addition to curbing of hemocyte proliferation in response to challenge with EBV DNA. Comparatively, upon injecting mice with EBV DNA, we detected enhanced expression of tumor necrosis factor-α (TNFα); this enhancement is rather comparable to IMD pathway activation in flies. This study hence indicates that D. melanogaster could possibly be utilized to identify immune mediators that may also play a role in the response to EBV DNA in higher systems.

Simulation of droplet impact onto a deep pool for large Froude numbers in different open-source codes

NASA Astrophysics Data System (ADS)

Korchagova, V. N.; Kraposhin, M. V.; Marchevsky, I. K.; Smirnova, E. V.

2017-11-01

A droplet impact on a deep pool can induce macro-scale or micro-scale effects like a crown splash, a high-speed jet, formation of secondary droplets or thin liquid films, etc. It depends on the diameter and velocity of the droplet, liquid properties, effects of external forces and other factors that a ratio of dimensionless criteria can account for. In the present research, we considered the droplet and the pool consist of the same viscous incompressible liquid. We took surface tension into account but neglected gravity forces. We used two open-source codes (OpenFOAM and Gerris) for our computations. We review the possibility of using these codes for simulation of processes in free-surface flows that may take place after a droplet impact on the pool. Both codes simulated several modes of droplet impact. We estimated the effect of liquid properties with respect to the Reynolds number and Weber number. Numerical simulation enabled us to find boundaries between different modes of droplet impact on a deep pool and to plot corresponding mode maps. The ratio of liquid density to that of the surrounding gas induces several changes in mode maps. Increasing this density ratio suppresses the crown splash.

Integrated Copy Number and Expression Analysis Identifies Profiles of Whole-Arm Chromosomal Alterations and Subgroups with Favorable Outcome in Ovarian Clear Cell Carcinomas

PubMed Central

Uehara, Yuriko; Oda, Katsutoshi; Ikeda, Yuji; Koso, Takahiro; Tsuji, Shingo; Yamamoto, Shogo; Asada, Kayo; Sone, Kenbun; Kurikawa, Reiko; Makii, Chinami; Hagiwara, Otoe; Tanikawa, Michihiro; Maeda, Daichi; Hasegawa, Kosei; Nakagawa, Shunsuke; Wada-Hiraike, Osamu; Kawana, Kei; Fukayama, Masashi; Fujiwara, Keiichi; Yano, Tetsu; Osuga, Yutaka; Fujii, Tomoyuki; Aburatani, Hiroyuki

2015-01-01

Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism analysis with 57 epithelial ovarian cancers (31 CCCs, 14 SCs, and 12 ECs) and microarray expression analysis with 55 cancers (25 CCCs, 16 SCs, and 14 ECs). We then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%; P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the CCC-1 and CCC-3 clusters (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%; P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis. PMID:26043110

ZENK expression in the auditory pathway of black-capped chickadees (Poecile atricapillus) as a function of D note number and duty cycle of chick-a-dee calls.

PubMed

Scully, Erin N; Schuldhaus, Brenna C; Congdon, Jenna V; Hahn, Allison H; Campbell, Kimberley A; Wilson, David R; Sturdy, Christopher B

2018-06-08

Black-capped chickadees (Poecile atricapillus) use their namesake chick-a-dee call for multiple functions, altering the features of the call depending on context. For example, duty cycle (the proportion of time filled by vocalizations) and fine structure traits (e.g., number of D notes) can encode contextual factors, such as predator size and food quality. Wilson and Mennill [1] found that chickadees show stronger behavioral responses to playback of chick-a-dee calls with higher duty cycles, but not to the number of D notes. That is, independent of the number of D notes in a call, but dependent on the overall proportion of time filled with vocalization, birds responded more to higher duty cycle playback compared to lower duty cycle playback. Here we presented chickadees with chick-a-dee calls that contained either two D (referred to hereafter as 2 D) notes with a low duty cycle, 2 D notes with a high duty cycle, 10 D notes with a high duty cycle, or 2 D notes with a high duty cycle but played in reverse (a non-signaling control). We then measured ZENK expression in the auditory nuclei where perceptual discrimination is thought to occur. Based on the behavioral results of Wilson and Mennill [1], we predicted we would observe the highest ZENK expression in response to forward-playing calls with high duty cycles; we predicted we would observe no significant difference in ZENK expression between forward-playing high duty cycle playbacks (2 D or 10 D). We found no significant difference between forward-playing 2 D and 10 D high duty cycle playbacks. However, contrary to our predictions, we did not find any effects of altering the duty cycle or note number presented. Copyright © 2018 Elsevier B.V. All rights reserved.

Maternal high-protein diet during pregnancy, but not during suckling, induced altered expression of an increasing number of hepatic genes in adult mouse offspring.

PubMed

Vanselow, Jens; Kucia, Marzena; Langhammer, Martina; Koczan, Dirk; Metges, Cornelia C

2016-04-01

Indirect effects of a high-protein maternal diet are not well understood. In this study, we analyzed short-term and sustainable effects of a prenatal versus early postnatal maternal high-protein diet on growth and hepatic gene expression in mouse offspring. Dams were exposed to an isoenergetic high-protein (HP, 40 % w/w) diet during pregnancy or lactation. Growth and hepatic expression profiles of male offspring were evaluated directly after weaning and 150 days after birth. Offspring from two dietary groups, high-protein diet during pregnancy and control diet during lactation (HPC), and control diet during pregnancy and high-protein diet during lactation (CHP), were compared with offspring (CC) from control-fed dams. Maternal CHP treatment was associated with sustained offspring growth retardation, but decreased numbers of affected hepatic genes in adults compared to weanlings. In contrast, offspring of the HPC group did not show persistent effects on growth parameters, but the number of affected hepatic genes was even increased at adult age. In both dietary groups, however, only a small subset of genes was affected in weanlings as well as in adults. We conclude that (1) prenatal and early postnatal maternal HP diet caused persistent, but (2) different effects and partially complementary trends on growth characteristics and on the hepatic transcriptome and associated pathways and that (3) only a small number of genes and associated upstream regulators might be involved in passing early diet-induced imprints to adulthood.

Multiple Long-Time Solutions for Intermediate Reynolds Number Flow past a Circular Cylinder with a Nonlinear Inertial and Dissipative Attachment

NASA Astrophysics Data System (ADS)

Blanchard, Antoine B. E.; Bergman, Lawrence A.; Vakakis, Alexander F.; Pearlstein, Arne J.

2016-11-01

We consider two-dimensional flow past a linearly-sprung cylinder allowed to undergo rectilinear motion normal to the mean flow, with an attached "nonlinear energy sink" consisting of a mass allowed to rotate about the cylinder axis, and whose rotational motion is linearly damped by a viscous damper. For Re < 50, where the flow is expected to be two-dimensional, we use different inlet transients to identify multiple long-time solutions, and to study how they depend on Re and a dimensionless spring constant. For fixed values of the ratio of cylinder density to fluid density, dimensionless damping coefficient, and ratio of the rotating mass to the total mass, we find that different inlet transients lead to different long-time solutions, including solutions that are steady and symmetric (with a motionless cylinder), time-periodic, quasi-periodic, and chaotic. The results show that over a wide range of the parameters, the steady symmetric motionless-cylinder solution is locally, but not globally, stable. Supported by NSF Grant CMMI-1363231.

Fast Magnetic Micropropellers with Random Shapes

PubMed Central

2015-01-01

Studying propulsion mechanisms in low Reynolds number fluid has implications for many fields, ranging from the biology of motile microorganisms and the physics of active matter to micromixing in catalysis and micro- and nanorobotics. The propulsion of magnetic micropropellers can be characterized by a dimensionless speed, which solely depends on the propeller geometry for a given axis of rotation. However, this dependence has so far been only investigated for helical propeller shapes, which were assumed to be optimal. In order to explore a larger variety of shapes, we experimentally studied the propulsion properties of randomly shaped magnetic micropropellers. Surprisingly, we found that their dimensionless speeds are high on average, comparable to previously reported nanofabricated helical micropropellers. The highest dimensionless speed we observed is higher than that of any previously reported propeller moving in a low Reynolds number fluid, proving that physical random shape generation can be a viable optimization strategy. PMID:26383225

Low Reynolds number kappa-epsilon and empirical transition models for oscillatory pipe flow and heat transfer. M.S. Thesis

NASA Technical Reports Server (NTRS)

Bauer, Christopher

1993-01-01

Stirling engine heat exchangers are shell-and-tube type with oscillatory flow (zero-mean velocity) for the inner fluid. This heat transfer process involves laminar-transition turbulent flow motions under oscillatory flow conditions. A low Reynolds number kappa-epsilon model, (Lam-Bremhorst form), was utilized in the present study to simulate fluid flow and heat transfer in a circular tube. An empirical transition model was used to activate the low Reynolds number k-e model at the appropriate time within the cycle for a given axial location within the tube. The computational results were compared with experimental flow and heat transfer data for: (1) velocity profiles, (2) kinetic energy of turbulence, (3) skin friction factor, (4) temperature profiles, and (5) wall heat flux. The experimental data were obtained for flow in a tube (38 mm diameter and 60 diameter long), with the maximum Reynolds number based on velocity being Re(sub max) = 11840, a dimensionless frequency (Valensi number) of Va = 80.2, at three axial locations X/D = 16, 30 and 44. The agreement between the computations and the experiment is excellent in the laminar portion of the cycle and good in the turbulent portion. Moreover, the location of transition was predicted accurately. The Low Reynolds Number kappa-epsilon model, together with an empirical transition model, is proposed herein to generate the wall heat flux values at different operating parameters than the experimental conditions. Those computational data can be used for testing the much simpler and less accurate one dimensional models utilized in 1-D Stirling Engine design codes.

The decay widths, the decay constants, and the branching fractions of a resonant state

NASA Astrophysics Data System (ADS)

de la Madrid, Rafael

2015-08-01

We introduce the differential and the total decay widths of a resonant (Gamow) state decaying into a continuum of stable states. When the resonance has several decay modes, we introduce the corresponding partial decay widths and branching fractions. In the approximation that the resonance is sharp, the expressions for the differential, partial and total decay widths of a resonant state bear a close resemblance with the Golden Rule. In such approximation, the branching fractions of a resonant state are the same as the standard branching fractions obtained by way of the Golden Rule. We also introduce dimensionless decay constants along with their associated differential decay constants, and we express experimentally measurable quantities such as the branching fractions and the energy distributions of decay events in terms of those dimensionless decay constants.

Expression levels of the receptor activator of NF-κB ligand and osteoprotegerin and the number of gram-negative bacteria in symptomatic and asymptomatic periapical lesions.

PubMed

Carneiro, E; Parolin, A B; Wichnieski, C; Rosa, E A R; Silva Neto, U X; Westphalen, V P D; Fariniuk, L F; Johann, A C B R

2017-01-01

The study aimed to verify the potential correlation between the detected amount of gram-negative bacteria and the radiographic sizes of the lesions in patients with symptomatic and asymptomatic apical periodontitis. Furthermore, to evaluate whether the expression of receptor activator of NF-κB ligand (RANKL) and osteoprotegerin (OPG) and the RANKL/OPG ratio are differentially regulated in both groups. Twenty patients with periapical lesions were divided into two groups: symptomatic (SYM) n=10 and asymptomatic (ASYM) n=10. After periapical surgery, the lesions were collected and processed for histological examination, and immunohistochemistry. The percentage of RANKL- and OPG-immunopositive areas relative to the total area of the microscopic field was calculated. For gram staining, the number of gram-negative cells per microscopic field was assessed. The radiographs of each patient were processed and measured. The Student's t-test and the Pearson correlation coefficient were performed. The SYM group showed a significantly higher number of gram-negative cells (p=0.007) when compared to the ASYM group. A higher number of gram-negative bacteria occurred more frequently in larger periapical lesions and the SYM group (p=0.03). The expression for RANKL and OPG and the RANKL/OPG ratio were not significantly different between the groups. There was a significant positive correlation between the number of bacteria and OPG levels in the SYM group (p=0.01). The number of bacteria seems to influence the symptoms and the radiographic size of a periapical lesion. Gram-negative bacteria may play an important role in OPG activity in the SYM group. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of the Performance of Heat Pipes and Phase-Change Materials with Multiple Localized Heat Sources for Space Applications

DTIC Science & Technology

1989-05-01

NUMERICAL ANALYSIS OF STEFAN PROBLEMS FOR GENERALIZED MULTI- DIMENSIONAL PHASE-CHANGE STRUCTURES USING THE ENTHALPY TRANSFORMING MODEL 4.1 Summary...equation St Stefan number, cs(Tm-Tw)/H or cs(Tm-Ti)/H s circumferential distance coordinate, m, Section III s dimensionless interface position along...fluid, kg/m 3 0 viscous dissipation term in the energy eqn. (1.4), Section I; dummy variable, Section IV r dimensionless time, ta/L 2 a Stefan -Boltzmann

On the fine-structure constant in a plasma model of the fluctuating vacuum substratum

NASA Technical Reports Server (NTRS)

Cragin, B. L.

1986-01-01

The existence of an intimate connection between the quivering motion of electrons and positrons (Zitterbewegung), predicted by the Dirac equation, and the zero-point fluctuations of the vacuum is suggested. The nature of the proposed connection is discussed quantitatively, and an approximate self-consistency relation is derived, supplying a purely mathematical expression that relates the dimensionless coupling strengths (fine-structure constants) alpha sub e and alpha sub g of electromagnetism and gravity. These considerations provide a tentative explanation for the heretofore puzzling number 1/alpha sub e of about 137.036 and suggest that attempts to unify gravity with the electroweak and strong interactions will ultimately prove successful.

PD-L1 (CD274) copy number gain, expression, and immune cell infiltration as candidate predictors for response to immune checkpoint inhibitors in soft-tissue sarcoma

PubMed Central

Budczies, Jan; Mechtersheimer, Gunhild; Denkert, Carsten; Klauschen, Frederick; Jöhrens, Korinna; Endris, Volker; Lier, Amelie; Lasitschka, Felix; Penzel, Roland; Dietel, Manfred; Brors, Benedikt; Gröschel, Stefan; Glimm, Hanno; Schirmacher, Peter; Renner, Marcus; Fröhling, Stefan; Stenzinger, Albrecht

2017-01-01

ABSTRACT Soft-tissue sarcomas (STS) are rare malignancies that account for 1% of adult cancers and comprise more than 50 entities. Current therapeutic options for advanced-stage STS are limited. Immune checkpoint inhibitors targeting the PD-1/PD-L1 signaling axis are being explored as new treatment modality in STS; however, the determinants of response to these agents are largely unknown. Using the sarcoma data set of The Cancer Genome Altas (TCGA) and an independent cohort of untreated high-grade STS, we analyzed DNA copy number status and mRNA expression of PD-L1 in a total of 335 STS cases. Copy number gains (CNG) were detected in 54 TCGA cases (21.1%), of which 21 (8.2%) harbored focal PD-L1 CNG and that were most prevalent in myxofibrosarcoma (35%) and undifferentiated pleomorphic sarcoma (34%). In the untreated high-grade STS cohort, we detected CNG in six cases (7.6%). Analysis of co-amplified genes identified a 5.6-Mb core region comprising 27 genes, including JAK2. Patients with PD-L1 CNG had higher PD-L1 expression compared with STS without CNG (fold change, 1.8; p = 0.02), an effect that was most pronounced in the setting of focal PD-L1 CNG (fold change, 3.0; p = 0.0027). STS with PD-L1 CNG showed a significantly higher mutational load compared with tumors with a diploid PD-L1 locus (median number of mutated genes; 58 vs. 40; p = 3.6E-06), and PD-L1 CNG were associated with inferior survival (HR = 1.82; p = 0.025). In contrast, T-cell infiltrates quantified by mRNA expression of CD3Z were associated with improved survival (HR = 0.88; p = 0.024) and consequently influenced the prognostic power of PD-L1 CNG, with low CD3Z levels conferring poor survival in cases with PD-L1 CNG (HR = 1.8; p = 0.049). These data demonstrate that PD-L1 GNG and elevated expression of PD-L1 occur in a substantial proportion of STS, have prognostic impact that is modulated by T-cell infiltrates, and thus warrant investigation as response predictors for immune checkpoint

PD-L1 (CD274) copy number gain, expression, and immune cell infiltration as candidate predictors for response to immune checkpoint inhibitors in soft-tissue sarcoma.

PubMed

Budczies, Jan; Mechtersheimer, Gunhild; Denkert, Carsten; Klauschen, Frederick; Mughal, Sadaf S; Chudasama, Priya; Bockmayr, Michael; Jöhrens, Korinna; Endris, Volker; Lier, Amelie; Lasitschka, Felix; Penzel, Roland; Dietel, Manfred; Brors, Benedikt; Gröschel, Stefan; Glimm, Hanno; Schirmacher, Peter; Renner, Marcus; Fröhling, Stefan; Stenzinger, Albrecht

2017-01-01

Soft-tissue sarcomas (STS) are rare malignancies that account for 1% of adult cancers and comprise more than 50 entities. Current therapeutic options for advanced-stage STS are limited. Immune checkpoint inhibitors targeting the PD-1/PD-L1 signaling axis are being explored as new treatment modality in STS; however, the determinants of response to these agents are largely unknown. Using the sarcoma data set of The Cancer Genome Altas (TCGA) and an independent cohort of untreated high-grade STS, we analyzed DNA copy number status and mRNA expression of PD-L1 in a total of 335 STS cases. Copy number gains (CNG) were detected in 54 TCGA cases (21.1%), of which 21 (8.2%) harbored focal PD-L1 CNG and that were most prevalent in myxofibrosarcoma (35%) and undifferentiated pleomorphic sarcoma (34%). In the untreated high-grade STS cohort, we detected CNG in six cases (7.6%). Analysis of co-amplified genes identified a 5.6-Mb core region comprising 27 genes, including JAK2 . Patients with PD-L1 CNG had higher PD-L1 expression compared with STS without CNG (fold change, 1.8; p = 0.02), an effect that was most pronounced in the setting of focal PD-L1 CNG (fold change, 3.0; p = 0.0027). STS with PD-L1 CNG showed a significantly higher mutational load compared with tumors with a diploid PD-L1 locus (median number of mutated genes; 58 vs. 40; p = 3.6E-06), and PD-L1 CNG were associated with inferior survival (HR = 1.82; p = 0.025). In contrast, T-cell infiltrates quantified by mRNA expression of CD3Z were associated with improved survival (HR = 0.88; p = 0.024) and consequently influenced the prognostic power of PD-L1 CNG, with low CD3Z levels conferring poor survival in cases with PD-L1 CNG (HR = 1.8; p = 0.049). These data demonstrate that PD-L1 GNG and elevated expression of PD-L1 occur in a substantial proportion of STS, have prognostic impact that is modulated by T-cell infiltrates, and thus warrant investigation as response predictors for immune checkpoint inhibition.

CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level

PubMed Central

Yuen, Garmen; Khan, Fehad J.; Gao, Shaojian; Stommel, Jayne M.; Batchelor, Eric; Wu, Xiaolin

2017-01-01

Abstract CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence. Kinetic analysis revealed that most target mutation occurs between 5 and 10 days following Cas9/sgRNA transduction, while sgRNAs with different potencies differ by their knockout time course and by their terminal-phase knockout efficiency. We showed that prolonged, low level expression of Cas9 and sgRNA often fails to elicit target mutation, particularly if the potency of the sgRNA is also low. Our findings provide new insights into the behavior of CRISPR/Cas9 in mammalian cells that could be used for future improvement of this platform. PMID:29036671

CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level.

PubMed

Yuen, Garmen; Khan, Fehad J; Gao, Shaojian; Stommel, Jayne M; Batchelor, Eric; Wu, Xiaolin; Luo, Ji

2017-11-16

CRISPR/Cas9 is a powerful gene editing tool for gene knockout studies and functional genomic screens. Successful implementation of CRISPR often requires Cas9 to elicit efficient target knockout in a population of cells. In this study, we investigated the role of several key factors, including variation in target copy number, inherent potency of sgRNA guides, and expression level of Cas9 and sgRNA, in determining CRISPR knockout efficiency. Using isogenic, clonal cell lines with variable copy numbers of an EGFP transgene, we discovered that CRISPR knockout is relatively insensitive to target copy number, but is highly dependent on the potency of the sgRNA guide sequence. Kinetic analysis revealed that most target mutation occurs between 5 and 10 days following Cas9/sgRNA transduction, while sgRNAs with different potencies differ by their knockout time course and by their terminal-phase knockout efficiency. We showed that prolonged, low level expression of Cas9 and sgRNA often fails to elicit target mutation, particularly if the potency of the sgRNA is also low. Our findings provide new insights into the behavior of CRISPR/Cas9 in mammalian cells that could be used for future improvement of this platform. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

Characterization of rarefaction waves in van der Waals fluids

NASA Astrophysics Data System (ADS)

Yuen, Albert; Barnard, John J.

2015-12-01

We calculate the isentropic evolution of an instantaneously heated foil, assuming a van der Waals equation of state with the Maxwell construction. The analysis by Yuen and Barnard [Phys. Rev. E 92, 033019 (2015), 10.1103/PhysRevE.92.033019] is extended for the particular case of three degrees of freedom. We assume heating to temperatures in the vicinity of the critical point. The self-similar profiles of the rarefaction waves describing the evolution of the foil display plateaus in density and temperature due to a phase transition from the single-phase to the two-phase regime. The hydrodynamic equations are expressed in a dimensionless form and the solutions form a set of universal curves, depending on a single parameter: the dimensionless initial entropy. We characterize the rarefaction waves by calculating how the plateau length, density, pressure, temperature, velocity, internal energy, and sound speed vary with dimensionless initial entropy.

Dosage-based parameters for characterization of puff dispersion results.

PubMed

Berbekar, Eva; Harms, Frank; Leitl, Bernd

2015-01-01

A set of parameters is introduced to characterize the dispersion of puff releases based on the measured dosage. These parameters are the dosage, peak concentration, arrival time, peak time, leaving time, ascent time, descent time and duration. Dimensionless numbers for the scaling of the parameters are derived from dimensional analysis. The dimensionless numbers are tested and confirmed based on a statistically representative wind tunnel dataset. The measurements were carried out in a 1:300 scale model of the Central Business District in Oklahoma City. Additionally, the effect of the release duration on the puff parameters is investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

FOXP3-expressing CD4(+) T-cell numbers increase in areas of duodenal gastric metaplasia and are associated to CD4(+) T-cell aggregates in the duodenum of Helicobacter pylori-infected duodenal ulcer patients.

PubMed

Kindlund, Bert; Sjöling, Asa; Hansson, Malin; Edebo, Anders; Hansson, Lars-Erik; Sjövall, Henrik; Svennerholm, Ann-Mari; Lundin, B Samuel

2009-06-01

We have previously demonstrated that Helicobacter pylori infection is associated with an increased number of CD4(+)CD25(high) regulatory T cells in the gastric and duodenal mucosa. In this study, we determined the number and localization of CD4(+) cells expressing the regulatory T-cell-specific transcription factor FOXP3 in the antrum and duodenum of duodenal ulcer patients, asymptomatic carriers, and uninfected individuals. We also determined gene expression levels of FOXP3 as well as anti- and proinflammatory cytokines before and after H. pylori eradication. Cellular FOXP3 expression was studied by immunofluorescence and flow cytometry, and transcription levels of FOXP3, interleukin (IL)-10, transforming growth factor-beta, CD4, and interferon-gamma were analyzed by real-time reverse transcription-polymerase chain reaction. We found an increased (6-fold) frequency of CD4(+)FOXP3(+) T cells in H. pylori-infected gastric mucosa; interestingly 26% of these cells did not co-express CD25. The increase of FOXP3-expressing T cells in the antrum of infected individuals was dependent on the presence of H. pylori, since eradication therapy resulted in 4-fold lower levels of FOXP3 and IL-10 mRNA in the antrum. Furthermore, higher numbers of CD4(+)FOXP3(+) T cells were found in areas of duodenal gastric metaplasia in the duodenum of duodenal ulcer patients compared to duodenal gastric metaplasia of asymptomatic individuals and healthy mucosa in both patient groups. In duodenal ulcer patients, the CD4(+)FOXP3(+) T cells were more highly associated to aggregates in the duodenal mucosa. The numbers of CD4(+)FOXP3(+) T cells are increased and localized in CD4(+) T-cell aggregates in areas of duodenal gastric metaplasia in duodenal ulcer patients.

Number of Langerhans cells is decreased in premalignant keratosis and skin cancers.

PubMed

Shevchuk, Z; Filip, A; Shevchuk, V; Kashuba, E

2014-03-01

It was shown earlier that a number of CD207 positive Langerhans cells was lower in basal cell carcinomas than in the normal epidermis. Moreover, benign skin lesions presented a higher number of Langerhans cells when they were compared to malignant tumors. To count Langerhans cells, assessing expression levels of CD1A and CD207 markers in actinic keratosis, basal and squamous cell carcinomas, compared with the normal skin. Comparison of Langerhans cells might give a valuable prognostic marker for skin cancer. Immunohistochemistry and methods of statistics were used. Expression of CD1A and CD207 markers was assessed in tumor samples of actinic keratosis, cutaneous basal and squamous cell carcinomas, in comparison with the normal skin. In each cohort there were 40 patients (and 11 healthy individuals). We have shown that the number of Langerhans cells is considerably lower in cutaneous basal and squamous cell carcinomas, compared with their number in the normal skin (p < 0.0001). CD1A expression correlated with CD207 expression only in the control group. There was no correlation in actinic keratosis, basal and squamous cell carcinoma. This may suggest an alteration of Langerhans cells phenotype in skin neoplastic diseases, making the number of Langerhans cells a valuable prognostic factor for skin tumors.

Shear-induced clustering of Brownian colloids in associative polymer networks at moderate Péclet number

NASA Astrophysics Data System (ADS)

Kim, Juntae; Helgeson, Matthew E.

2016-08-01

We investigate shear-induced clustering and its impact on fluid rheology in polymer-colloid mixtures at moderate colloid volume fraction. By employing a thermoresponsive system that forms associative polymer-colloid networks, we present experiments of rheology and flow-induced microstructure on colloid-polymer mixtures in which the relative magnitudes of the time scales associated with relaxation of viscoelasticity and suspension microstructure are widely and controllably varied. In doing so, we explore several limits of relative magnitude of the relevant dimensionless shear rates, the Weissenberg number Wi and the Péclet number Pe. In all of these limits, we find that the fluid exhibits two distinct regimes of shear thinning at relatively low and high shear rates, in which the rheology collapses by scaling with Wi and Pe, respectively. Using three-dimensionally-resolved flow small-angle neutron scattering measurements, we observe clustering of the suspension above a critical shear rate corresponding to Pe ˜0.1 over a wide range of fluid conditions, having anisotropy with projected orientation along both the vorticity and compressional axes of shear. The degree of anisotropy is shown to scale with Pe. From this we formulate an empirical model for the shear stress and viscosity, in which the viscoelastic network stress is augmented by an asymptotic shear thickening contribution due to hydrodynamic clustering. Overall, our results elucidate the significant role of hydrodynamic interactions in contributing to shear-induced clustering of Brownian suspensions in viscoelastic liquids.

Increased numbers of pre-existing memory CD8 T cells and decreased T-bet expression can restrain terminal differentiation of secondary effector and memory CD8 T cells1

PubMed Central

Joshi, Nikhil S.; Cui, Weiguo; Dominguez, Claudia; Chen, Jonathan H.; Hand, Timothy W.; Kaech, Susan M.

2011-01-01

Memory CD8 T cells acquire TEM properties following reinfection, and may reach terminally differentiated, senescent states (“Hayflick limit”) after multiple infections. The signals controlling this process are not well understood, but we found that the degree of 2o effector and memory CD8 T cell differentiation was intimately linked to the amount of T-bet expressed upon reactivation and pre-existing memory CD8 T cell number (i.e., 1o memory CD8 T cell precursor frequency) present during secondary infection. Compared to naïve cells, memory CD8 T cells were predisposed towards terminal effector (TE) cell differentiation because they could immediately respond to IL-12 and induce T-bet, even in the absence of antigen. TE cell formation following 2o or 3o infections was dependent on increased T-bet expression because T-bet+/− cells were resistant to these phenotypic changes. Larger numbers of pre-existing memory CD8 T cells limited the duration of 2o infection and the amount of IL-12 produced, and consequently, this reduced T-bet expression and the proportion of 2o TE CD8 T cells that formed. Together, these data show that, over repeated infections, memory CD8 T cell quality and proliferative fitness is not strictly determined by the number of serial encounters with antigen or cell divisions, but is a function of the CD8 T cell differentiation state, which is genetically controlled in a T-bet-dependent manner. This differentiation state can be modulated by pre-existing memory CD8 T cell number and the intensity of inflammation during reinfection. These results have important implications for vaccinations involving prime-boost strategies. PMID:21930973

Functional effects of CCL3L1 copy number.

PubMed

Carpenter, D; McIntosh, R S; Pleass, R J; Armour, J A L

2012-07-01

Copy number variation (CNV) is becoming increasingly important as a feature of human variation in disease susceptibility studies. However, the consequences of CNV are not so well understood. Here, we present data exploring the functional consequences of CNV of CCL3L1 in 55 independent UK samples with no known clinical phenotypes. The copy number of CCL3L1 was determined by the paralogue ratio test, and expression levels of macrophage inflammatory protein-1α (MIP-1α) and mRNA from stimulated monocytes were measured and analysed. The data show no statistically significant association of MIP-1α protein levels with copy number. However, there was a significant correlation between copy number and CCL3L1:CCL3 mRNA ratio. The data also provide evidence that expression of CCL3 predominates in both protein and mRNA, and therefore the observed variation of CCL3 is potentially more important biologically than that of CNV of CCL3L1.

Isothermal laminar fluid flow in spiral tube coils

NASA Astrophysics Data System (ADS)

Patil, Rahul Harishchandra

2018-06-01

An experimental study is performed to measure pressure drop for Newtonian fluid flow through copper spirals of different geometries. The experimental friction factors obtained are presented and correlated with the different geometrical parameters of the spiral coils. Four spiral coils with (D_i/D) ratio ranging from 0.0178 to 0.028 and (L/D_i) ratio ranging from 527.5 to 2110.169 are investigated. A new dimensionless number, the R number is introduced which is found to characterize the fluid flow phenomenon in spiral coil tubes. An innovative approach to correlate Dean and R numbers with friction factor data of variable curvature coils for laminar flow regime is presented for the first time. The study will prove useful to bridge the gap between the straight tube flow and curved coil flow based on a single dimensionless number.

The Kirchhoff index and the matching number

NASA Astrophysics Data System (ADS)

Zhou, Bo; Trinajstić, Nenad

The Kirchhoff index of a connected (molecular) graph is the sum of the resistance-distances between all unordered pairs of vertices and may also be expressed by its Laplacian eigenvalues. We determine the minimum Kirchhoff index of connected (molecular) graphs in terms of the number of vertices and matching number and characterize the unique extremal graph. The results on the Kirchhoff index are compared with the corresponding results on the Wiener index.

Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.

PubMed

Goldstein, Darlene R

2006-10-01

Studies of gene expression using high-density short oligonucleotide arrays have become a standard in a variety of biological contexts. Of the expression measures that have been proposed to quantify expression in these arrays, multi-chip-based measures have been shown to perform well. As gene expression studies increase in size, however, utilizing multi-chip expression measures is more challenging in terms of computing memory requirements and time. A strategic alternative to exact multi-chip quantification on a full large chip set is to approximate expression values based on subsets of chips. This paper introduces an extrapolation method, Extrapolation Averaging (EA), and a resampling method, Partition Resampling (PR), to approximate expression in large studies. An examination of properties indicates that subset-based methods can perform well compared with exact expression quantification. The focus is on short oligonucleotide chips, but the same ideas apply equally well to any array type for which expression is quantified using an entire set of arrays, rather than for only a single array at a time. Software implementing Partition Resampling and Extrapolation Averaging is under development as an R package for the BioConductor project.

Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome.

PubMed

Bassett, Anne S; Lowther, Chelsea; Merico, Daniele; Costain, Gregory; Chow, Eva W C; van Amelsvoort, Therese; McDonald-McGinn, Donna; Gur, Raquel E; Swillen, Ann; Van den Bree, Marianne; Murphy, Kieran; Gothelf, Doron; Bearden, Carrie E; Eliez, Stephan; Kates, Wendy; Philip, Nicole; Sashi, Vandana; Campbell, Linda; Vorstman, Jacob; Cubells, Joseph; Repetto, Gabriela M; Simon, Tony; Boot, Erik; Heung, Tracy; Evers, Rens; Vingerhoets, Claudia; van Duin, Esther; Zackai, Elaine; Vergaelen, Elfi; Devriendt, Koen; Vermeesch, Joris R; Owen, Michael; Murphy, Clodagh; Michaelovosky, Elena; Kushan, Leila; Schneider, Maude; Fremont, Wanda; Busa, Tiffany; Hooper, Stephen; McCabe, Kathryn; Duijff, Sasja; Isaev, Karin; Pellecchia, Giovanna; Wei, John; Gazzellone, Matthew J; Scherer, Stephen W; Emanuel, Beverly S; Guo, Tingwei; Morrow, Bernice E; Marshall, Christian R

2017-11-01

Chromosome 22q11.2 deletion syndrome (22q11.2DS) is associated with a more than 20-fold increased risk for developing schizophrenia. The aim of this study was to identify additional genetic factors (i.e., "second hits") that may contribute to schizophrenia expression. Through an international consortium, the authors obtained DNA samples from 329 psychiatrically phenotyped subjects with 22q11.2DS. Using a high-resolution microarray platform and established methods to assess copy number variation (CNV), the authors compared the genome-wide burden of rare autosomal CNV, outside of the 22q11.2 deletion region, between two groups: a schizophrenia group and those with no psychotic disorder at age ≥25 years. The authors assessed whether genes overlapped by rare CNVs were overrepresented in functional pathways relevant to schizophrenia. Rare CNVs overlapping one or more protein-coding genes revealed significant between-group differences. For rare exonic duplications, six of 19 gene sets tested were enriched in the schizophrenia group; genes associated with abnormal nervous system phenotypes remained significant in a stepwise logistic regression model and showed significant interactions with 22q11.2 deletion region genes in a connectivity analysis. For rare exonic deletions, the schizophrenia group had, on average, more genes overlapped. The additional rare CNVs implicated known (e.g., GRM7, 15q13.3, 16p12.2) and novel schizophrenia risk genes and loci. The results suggest that additional rare CNVs overlapping genes outside of the 22q11.2 deletion region contribute to schizophrenia risk in 22q11.2DS, supporting a multigenic hypothesis for schizophrenia. The findings have implications for understanding expression of psychotic illness and herald the importance of whole-genome sequencing to appreciate the overall genomic architecture of schizophrenia.

Modulation of Mitochondrial DNA Copy Number to Induce Hepatocytic Differentiation of Human Amniotic Epithelial Cells.

PubMed

Vaghjiani, Vijesh; Cain, Jason E; Lee, William; Vaithilingam, Vijayaganapathy; Tuch, Bernard E; St John, Justin C

2017-10-15

Mitochondrial deoxyribonucleic acid (mtDNA) copy number is tightly regulated during pluripotency and differentiation. There is increased demand of cellular adenosine triphosphate (ATP) during differentiation for energy-intensive cell types such as hepatocytes and neurons to meet the cell's functional requirements. During hepatocyte differentiation, mtDNA copy number should be synchronously increased to generate sufficient ATP through oxidative phosphorylation. Unlike bone marrow mesenchymal cells, mtDNA copy number failed to increase by 28 days of differentiation of human amniotic epithelial cells (hAEC) into hepatocyte-like cells (HLC) despite their expression of some end-stage hepatic markers. This was due to higher levels of DNA methylation at exon 2 of POLGA, the mtDNA-specific replication factor. Treatment with a DNA demethylation agent, 5-azacytidine, resulted in increased mtDNA copy number, reduced DNA methylation at exon 2 of POLGA, and reduced hepatic gene expression. Depletion of mtDNA followed by subsequent differentiation did not increase mtDNA copy number, but reduced DNA methylation at exon 2 of POLGA and increased expression of hepatic and pluripotency genes. We encapsulated hAEC in barium alginate microcapsules and subsequently differentiated them into HLC. Encapsulation resulted in no net increase of mtDNA copy number but a significant reduction in DNA methylation of POLGA. RNAseq analysis showed that differentiated HLC express hepatocyte-specific genes but also increased expression of inflammatory interferon genes. Differentiation in encapsulated cells showed suppression of inflammatory genes as well as increased expression of genes associated with hepatocyte function pathways and networks. This study demonstrates that an increase in classical hepatic gene expression can be achieved in HLC through encapsulation, although they fail to effectively regulate mtDNA copy number.

Quantifying near-wall coherent structures in turbulent convection

NASA Astrophysics Data System (ADS)

Gunasegarane, G. S.; A Puthenveettil, Baburaj; K Agrawal, Yogesh; Schmeling, Daniel; Bosbach, Johannes; Arakeri, Jaywant; IIT Madras-DLR-IISc Collaboration

2011-11-01

We present planforms of line plumes formed on horizontal surfaces in turbulent convection, along with the length of near- wall line plumes measured from these planforms, in a six decade range of Rayleigh numbers (105 < Ra <1011) and at three Prandtl numbers (Pr = 0 . 7 , 6 , 602). Using geometric constraints on the relations for the mean plume spacings, we obtain expressions for the total length of these near-wall plumes in turbulent convection. The plume length per unit area (Lp / A), made dimensionless by the near-wall length scale in turbulent convection (Zw) remains a constant for a given fluid. The Nusselt number is shown to be directly proportional to Lp H / A for a given fluid layer of height H. Increase in Pr has a weak influence in decreasing Lp / A . These expressions match the measurements, thereby showing that the assumption of laminar natural convection boundary layers in turbulent convection is consistent with the observed total length of line plumes. We then show that similar relationships are obtained based on the assumption that the line plumes are the outcome of the instability of laminar natural convection boundary layers on the horizontal surfaces.

Inspection of the dynamic properties of laminar separation bubbles: free-stream turbulence intensity effects for different Reynolds numbers

NASA Astrophysics Data System (ADS)

Simoni, Daniele; Lengani, Davide; Ubaldi, Marina; Zunino, Pietro; Dellacasagrande, Matteo

2017-06-01

The effects of free-stream turbulence intensity (FSTI) on the transition process of a pressure-induced laminar separation bubble have been studied for different Reynolds numbers (Re) by means of time-resolved (TR) PIV. Measurements have been performed along a flat plate installed within a double-contoured test section, designed to produce an adverse pressure gradient typical of ultra-high-lift turbine blade profiles. A test matrix spanning 3 FSTI levels and 3 Reynolds numbers has been considered allowing estimation of cross effects of these parameters on the instability mechanisms driving the separated flow transition process. Boundary layer integral parameters, spatial growth rate and saturation level of velocity fluctuations are discussed for the different cases in order to characterize the base flow response as well as the time-mean properties of the Kelvin-Helmholtz instability. The inspection of the instantaneous velocity vector maps highlights the dynamics of the large-scale structures shed near the bubble maximum displacement, as well as the low-frequency motion of the fore part of the separated shear layer. Proper Orthogonal Decomposition (POD) has been implemented to reduce the large amount of data for each condition allowing a rapid evaluation of the group velocity, spatial wavelength and dominant frequency of the vortex shedding process. The dimensionless shedding wave number parameter makes evident that the modification of the shear layer thickness at separation due to Reynolds number variation mainly drives the length scale of the rollup vortices, while higher FSTI levels force the onset of the shedding phenomenon to occur upstream due to the higher velocity fluctuations penetrating into the separating boundary layer.

Estimating flood hydrographs for urban basins in North Carolina

USGS Publications Warehouse

Mason, R.R.; Bales, J.D.

1996-01-01

A dimensionless hydrograph for North Carolina was developed from data collected in 29 urban and urbanizing basins in the State. The dimen- sionless hydrograph can be used with an estimate of peak flow and basin lagtime to synthesize a design flood hydrograph for urban basins in North Carolina. Peak flows can be estimated from a number of avail- able techniques; a procedure for estimating basin lagtime from main channel length, stream slope, and percentage of impervious area was developed from data collected at 50 sites and is presented in this report. The North Carolina dimensionless hydrograph provides satis- factory predictions of flood hydrographs in all regions of the State except for basins in or near Asheville where the method overestimated 11 of 12 measured hydrographs. A previously developed dimensionless hydrograph for urban basins in the Piedmont and upper Coastal Plain of South Carolina provides better flood-hydrograph predictions for the Asheville basins and has a standard error of 21 percent as compared to 41 percent for the North Carolina dimensionless hydrograph.

Low-rank regularization for learning gene expression programs.

PubMed

Ye, Guibo; Tang, Mengfan; Cai, Jian-Feng; Nie, Qing; Xie, Xiaohui

2013-01-01

Learning gene expression programs directly from a set of observations is challenging due to the complexity of gene regulation, high noise of experimental measurements, and insufficient number of experimental measurements. Imposing additional constraints with strong and biologically motivated regularizations is critical in developing reliable and effective algorithms for inferring gene expression programs. Here we propose a new form of regulation that constrains the number of independent connectivity patterns between regulators and targets, motivated by the modular design of gene regulatory programs and the belief that the total number of independent regulatory modules should be small. We formulate a multi-target linear regression framework to incorporate this type of regulation, in which the number of independent connectivity patterns is expressed as the rank of the connectivity matrix between regulators and targets. We then generalize the linear framework to nonlinear cases, and prove that the generalized low-rank regularization model is still convex. Efficient algorithms are derived to solve both the linear and nonlinear low-rank regularized problems. Finally, we test the algorithms on three gene expression datasets, and show that the low-rank regularization improves the accuracy of gene expression prediction in these three datasets.

Steroid Treatment Reduces Allergic Airway Inflammation and Does Not Alter the Increased Numbers of Dendritic Cells and Calcitonin Gene-Related Peptide-Expressing Neurons in Airway Sensory Ganglia.

PubMed

Le, Duc Dung; Funck, Ulrike; Wronski, Sabine; Heck, Sebastian; Tschernig, Thomas; Bischoff, Markus; Sester, Martina; Herr, Christian; Bals, Robert; Welte, Tobias; Braun, Armin; Dinh, Quoc Thai

2016-01-01

Our previous data demonstrated that allergic airway inflammation induces migration of dendritic cells (DC) into airway sensory jugular and nodose ganglia (jugular-nodose ganglion complex; JNC). Here we investigated the effects of steroid treatment regarding the expression and migration of DC and calcitonin gene-related peptide (CGRP)-immunoreactive neurons of vagal sensory ganglia during allergic airway inflammation. A house dust mite (HDM) model for allergic airway inflammation was used. The mice received 0.3 mg fluticasone propionate per kilogram of body weight in the last 9 days. JNC slices were analyzed on MHC II, the neuronal marker PGP9.5, and the neuropeptide CGRP. Allergic airway inflammation increased the numbers of DC and CGRP-expressing neurons in the JNC significantly in comparison to the controls (DC/neurons: HDM 44.58 ± 1.6% vs. saline 33.29 ± 1.6%, p < 0.05; CGRP-positive neurons/total neurons: HDM 30.65 ± 1.9% vs. saline 19.49 ± 2.3%, p < 0.05). Steroid treatment did not have any effect on the numbers of DC and CGRP-expressing neurons in the JNC compared to HDM-treated mice. The present findings indicate an important role of DC and CGRP-containing neurons in the pathogenesis of allergic airway inflammation. However, steroid treatment did not have an effect on the population of DC and neurons displaying CGRP in the JNC, whereas steroid treatment was found to suppress allergic airway inflammation. © 2015 S. Karger AG, Basel.

The Development of Children's Expressive Drawing

ERIC Educational Resources Information Center

Jolley, Richard P.; Fenn, Kathryn; Jones, Luisa

2004-01-01

Two studies are presented on expressive happy and sad drawings made by British 4- to 12-year-olds (n = 80 and 160, respectively) in which the drawings were assessed individually for the quantity and quality of expressive devices. Quantity was measured in the number of appropriate expressive content themes and formal properties evident in each…

Beneath Our Feet: Strategies for Locomotion in Granular Media

NASA Astrophysics Data System (ADS)

Hosoi, A. E.; Goldman, Daniel I.

2015-01-01

“If you find yourself in a hole, stop digging.” Although Denis Healey's famous adage ( Metcalfe 2007 ) may offer sound advice for politicians, it is less relevant to worms, clams, and other higher organisms that rely on their digging ability for survival. In this article, we review recent work on the development of simple models that elucidate the fundamental principles underlying digging and burrowing strategies employed by biological systems. Four digging regimes are identified based on dimensionless digger size and the dimensionless inertial number. We select biological organisms to represent three of the four regimes: razor clams, sandfish, and nematodes. Models for all three diggers are derived and discussed, and analogies are drawn to low-Reynolds number swimmers.

Thermal radiation and mass transfer effects on unsteady MHD free convection flow past a vertical oscillating plate

NASA Astrophysics Data System (ADS)

Rana, B. M. Jewel; Ahmed, Rubel; Ahmmed, S. F.

2017-06-01

Unsteady MHD free convection flow past a vertical porous plate in porous medium with radiation, diffusion thermo, thermal diffusion and heat source are analyzed. The governing non-linear, partial differential equations are transformed into dimensionless by using non-dimensional quantities. Then the resultant dimensionless equations are solved numerically by applying an efficient, accurate and conditionally stable finite difference scheme of explicit type with the help of a computer programming language Compaq Visual Fortran. The stability and convergence analysis has been carried out to establish the effect of velocity, temperature, concentration, skin friction, Nusselt number, Sherwood number, stream lines and isotherms line. Finally, the effects of various parameters are presented graphically and discussed qualitatively.

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Numerical investigation of MHD flow with Soret and Dufour effect

NASA Astrophysics Data System (ADS)

Hayat, Tasawar; Nasir, Tehreem; Khan, Muhammad Ijaz; Alsaedi, Ahmed

2018-03-01

This paper describes the flow due to an exponentially curved surface subject to Soret and Dufour effects. Nonlinear velocity is considered. Exponentially curved stretchable sheet induced the flow. Fluid is electrical conducting through constant applied magnetic field. The governing flow expressions are reduced to ordinary ones and then tackled by numerical technique (Built-in-Shooting). Impacts of various flow variables on the dimensionless velocity, concentration and temperature fields are graphically presented and discussed in detail. Skin friction coefficient and Sherwood and Nusselt numbers are studied through graphs. Furthermore it is observed that Soret and Dufour variables regulate heat and mass transfer rates. It is also noteworthy that velocity decays for higher magnetic variable. Skin friction magnitude decays via curvature and magnetic variables. Also mass transfer gradient or rate of mass transport enhances for higher estimations of curvature parameter and Schmidt number.

Abstract number and arithmetic in preschool children.

PubMed

Barth, Hilary; La Mont, Kristen; Lipton, Jennifer; Spelke, Elizabeth S

2005-09-27

Educated humans use language to express abstract number, applying the same number words to seven apples, whistles, or sins. Is language or education the source of numerical abstraction? Claims to the contrary must present evidence for numerical knowledge that applies to disparate entities, in people who have received no formal mathematics instruction and cannot express such knowledge in words. Here we show that preschool children can compare and add large sets of elements without counting, both within a single visual-spatial modality (arrays of dots) and across two modalities and formats (dot arrays and tone sequences). In two experiments, children viewed animations and either compared one visible array of dots to a second array or added two successive dot arrays and compared the sum to a third array. In further experiments, a dot array was replaced by a sequence of sounds, so that participants had to integrate quantity information presented aurally and visually. Children performed all tasks successfully, without resorting to guessing strategies or responding to continuous variables. Their accuracy varied with the ratio of the two quantities: a signature of large, approximate number representations in adult humans and animals. Addition was as accurate as comparison, even though children showed no relevant knowledge when presented with symbolic versions of the addition tasks. Abstract knowledge of number and addition therefore precedes, and may guide, language-based instruction in mathematics.

Rethinking cell-cycle-dependent gene expression in Schizosaccharomyces pombe.

PubMed

Cooper, Stephen

2017-11-01

Three studies of gene expression during the division cycle of Schizosaccharomyces pombe led to the proposal that a large number of genes are expressed at particular times during the S. pombe cell cycle. Yet only a small fraction of genes proposed to be expressed in a cell-cycle-dependent manner are reproducible in all three published studies. In addition to reproducibility problems, questions about expression amplitudes, cell-cycle timing of expression, synchronization artifacts, and the problem with methods for synchronizing cells must be considered. These problems and complications prompt the idea that caution should be used before accepting the conclusion that there are a large number of genes expressed in a cell-cycle-dependent manner in S. pombe.

Quantity-activity relationship of denitrifying bacteria and environmental scaling in streams of a forested watershed

USGS Publications Warehouse

O'Connor, B.L.; Hondzo, Miki; Dobraca, D.; LaPara, T.M.; Finlay, J.A.; Brezonik, P.L.

2006-01-01

The spatial variability of subreach denitrification rates in streams was evaluated with respect to controlling environmental conditions, molecular examination of denitrifying bacteria, and dimensional analysis. Denitrification activities ranged from 0 and 800 ng-N gsed-1 d-1 with large variations observed within short distances (<50 m) along stream reaches. A log-normal probability distribution described the range in denitrification activities and was used to define low (16% of the probability distributibn), medium (68%), and high (16%) denitrification potential groups. Denitrifying bacteria were quantified using a competitive polymerase chain reaction (cPCR) technique that amplified the nirK gene that encodes for nitrite reductase. Results showed a range of nirK quantities from 103 to 107 gene-copy-number gsed.-1 A nonparametric statistical test showed no significant difference in nirK quantifies among stream reaches, but revealed that samples with a high denitrification potential had significantly higher nirK quantities. Denitrification activity was positively correlated with nirK quantities with scatter in the data that can be attributed to varying environmental conditions along stream reaches. Dimensional analysis was used to evaluate denitrification activities according to environmental variables that describe fluid-flow properties, nitrate and organic material quantities, and dissolved oxygen flux. Buckingham's pi theorem was used to generate dimensionless groupings and field data were used to determine scaling parameters. The resulting expressions between dimensionless NO3- flux and dimensionless groupings of environmental variables showed consistent scaling, which indicates that the subreach variability in denitrification rates can be predicted by the controlling physical, chemical, and microbiological conditions. Copyright 2006 by the American Geophysical Union.

Parametric number covariance in quantum chaotic spectra.

PubMed

Vinayak; Kumar, Sandeep; Pandey, Akhilesh

2016-03-01

We study spectral parametric correlations in quantum chaotic systems and introduce the number covariance as a measure of such correlations. We derive analytic results for the classical random matrix ensembles using the binary correlation method and obtain compact expressions for the covariance. We illustrate the universality of this measure by presenting the spectral analysis of the quantum kicked rotors for the time-reversal invariant and time-reversal noninvariant cases. A local version of the parametric number variance introduced earlier is also investigated.

Dimensional Analysis on Forest Fuel Bed Fire Spread.

PubMed

Yang, Jiann C

2018-01-01

A dimensional analysis was performed to correlate the fuel bed fire rate of spread data previously reported in the literature. Under wind condition, six pertinent dimensionless groups were identified, namely dimensionless fire spread rate, dimensionless fuel particle size, fuel moisture content, dimensionless fuel bed depth or dimensionless fuel loading density, dimensionless wind speed, and angle of inclination of fuel bed. Under no-wind condition, five similar dimensionless groups resulted. Given the uncertainties associated with some of the parameters used to estimate the dimensionless groups, the dimensionless correlations using the resulting dimensionless groups correlate the fire rates of spread reasonably well under wind and no-wind conditions.

Genomic DNA Copy-Number Alterations of the let-7 Family in Human Cancers

PubMed Central

Greshock, Joel; Shen, Liang; Yang, Xiaojun; Shao, Zhongjun; Liang, Shun; Tanyi, Janos L.; Sood, Anil K.; Zhang, Lin

2012-01-01

In human cancer, expression of the let-7 family is significantly reduced, and this is associated with shorter survival times in patients. However, the mechanisms leading to let-7 downregulation in cancer are still largely unclear. Since an alteration in copy-number is one of the causes of gene deregulation in cancer, we examined copy number alterations of the let-7 family in 2,969 cancer specimens from a high-resolution SNP array dataset. We found that there was a reduction in the copy number of let-7 genes in a cancer-type specific manner. Importantly, focal deletion of four let-7 family members was found in three cancer types: medulloblastoma (let-7a-2 and let-7e), breast cancer (let-7a-2), and ovarian cancer (let-7a-3/let-7b). For example, the genomic locus harboring let-7a-3/let-7b was deleted in 44% of the specimens from ovarian cancer patients. We also found a positive correlation between the copy number of let-7b and mature let-7b expression in ovarian cancer. Finally, we showed that restoration of let-7b expression dramatically reduced ovarian tumor growth in vitro and in vivo. Our results indicate that copy number deletion is an important mechanism leading to the downregulation of expression of specific let-7 family members in medulloblastoma, breast, and ovarian cancers. Restoration of let-7 expression in tumor cells could provide a novel therapeutic strategy for the treatment of cancer. PMID:22970210

Dimensional analysis of MINMOD leads to definition of the disposition index of glucose regulation and improved simulation algorithm.

PubMed

Nittala, Aparna; Ghosh, Soumitra; Stefanovski, Darko; Bergman, Richard; Wang, Xujing

2006-07-14

Frequently Sampled Intravenous Glucose Tolerance Test (FSIVGTT) together with its mathematical model, the minimal model (MINMOD), have become important clinical tools to evaluate the metabolic control of glucose in humans. Dimensional analysis of the model is up to now not available. A formal dimensional analysis of MINMOD was carried out and the degree of freedom of MINMOD was examined. Through re-expressing all state variable and parameters in terms of their reference scales, MINMOD was transformed into a dimensionless format. Previously defined physiological indices including insulin sensitivity, glucose effectiveness, and first and second phase insulin responses were re-examined in this new formulation. Further, the parameter estimation from FSIVGTT was implemented using both the dimensional and the dimensionless formulations of MINMOD, and the performances were compared utilizing Monte Carlo simulation as well as real human FSIVGTT data. The degree of freedom (DOF) of MINMOD was found to be 7. The model was maximally simplified in the dimensionless formulation that normalizes the variation in glucose and insulin during FSIVGTT. In the new formulation, the disposition index (Dl), a composite parameter known to be important in diabetes pathology, was naturally defined as one of the dimensionless parameters in the system. The numerical simulation using the dimensionless formulation led to a 1.5-5 fold gain in speed, and significantly improved accuracy and robustness in parameter estimation compared to the dimensional implementation. Dimensional analysis of MINMOD led to simplification of the model, direct identification of the important composite factors in the dynamics of glucose metabolic control, and better simulations algorithms.

Functional expression of an ajmaline pathway-specific esterase from Rauvolfia in a novel plant-virus expression system.

PubMed

Ruppert, Martin; Woll, Jörn; Giritch, Anatoli; Genady, Ezzat; Ma, Xueyan; Stöckigt, Joachim

2005-11-01

Acetylajmalan esterase (AAE) plays an essential role in the late stage of ajmaline biosynthesis. Based on the partial peptide sequences of AAE isolated and purified from Rauvolfia cell suspensions, a full-length AAE cDNA clone was isolated. The amino acid sequence of AAE has the highest level of identity of 40% to putative lipases known from the Arabidopsis thaliana genome project. Based on the primary structure AAE is a new member of the GDSL lipase superfamily. The expression in Escherichia coli failed although a wide range of conditions were tested. With a novel virus-based plant expression system, it was possible to express AAE functionally in leaves of Nicotiana benthamiana Domin. An extraordinarily high enzyme activity was detected in the Nicotiana tissue, which exceeded that in Rauvolfia serpentina (L.) Benth. ex Kurz cell suspension cultures about 20-fold. This expression allowed molecular analysis of AAE for the first time and increased the number of functionally expressed alkaloid genes from Rauvolfia now to eight, and the number of ajmaline pathway-specific cDNAs to a total of six.

Reproduction numbers for infections with free-living pathogens growing in the environment.

PubMed

Bani-Yaghoub, Majid; Gautam, Raju; Shuai, Zhisheng; van den Driessche, P; Ivanek, Renata

2012-01-01

The basic reproduction number ℛ(0) for a compartmental disease model is often calculated by the next generation matrix (NGM) approach. When the interactions within and between disease compartments are interpreted differently, the NGM approach may lead to different ℛ(0) expressions. This is demonstrated by considering a susceptible-infectious-recovered-susceptible model with free-living pathogen (FLP) growing in the environment. Although the environment could play different roles in the disease transmission process, leading to different ℛ(0) expressions, there is a unique type reproduction number when control strategies are applied to the host population. All ℛ(0) expressions agree on the threshold value 1 and preserve their order of magnitude. However, using data for salmonellosis and cholera, it is shown that the estimated ℛ(0) values are substantially different. This study highlights the utility and limitations of reproduction numbers to accurately quantify the effects of control strategies for infections with FLPs growing in the environment.

A method for generating new datasets based on copy number for cancer analysis.

PubMed

Kim, Shinuk; Kon, Mark; Kang, Hyunsik

2015-01-01

New data sources for the analysis of cancer data are rapidly supplementing the large number of gene-expression markers used for current methods of analysis. Significant among these new sources are copy number variation (CNV) datasets, which typically enumerate several hundred thousand CNVs distributed throughout the genome. Several useful algorithms allow systems-level analyses of such datasets. However, these rich data sources have not yet been analyzed as deeply as gene-expression data. To address this issue, the extensive toolsets used for analyzing expression data in cancerous and noncancerous tissue (e.g., gene set enrichment analysis and phenotype prediction) could be redirected to extract a great deal of predictive information from CNV data, in particular those derived from cancers. Here we present a software package capable of preprocessing standard Agilent copy number datasets into a form to which essentially all expression analysis tools can be applied. We illustrate the use of this toolset in predicting the survival time of patients with ovarian cancer or glioblastoma multiforme and also provide an analysis of gene- and pathway-level deletions in these two types of cancer.

Is Approximate Number Precision a Stable Predictor of Math Ability?

ERIC Educational Resources Information Center

Libertus, Melissa E.; Feigenson, Lisa; Halberda, Justin

2013-01-01

Previous research shows that children's ability to estimate numbers of items using their Approximate Number System (ANS) predicts later math ability. To more closely examine the predictive role of early ANS acuity on later abilities, we assessed the ANS acuity, math ability, and expressive vocabulary of preschoolers twice, six months apart. We…

The precision of mapping between number words and the approximate number system predicts children's formal math abilities.

PubMed

Libertus, Melissa E; Odic, Darko; Feigenson, Lisa; Halberda, Justin

2016-10-01

Children can represent number in at least two ways: by using their non-verbal, intuitive approximate number system (ANS) and by using words and symbols to count and represent numbers exactly. Furthermore, by the time they are 5years old, children can map between the ANS and number words, as evidenced by their ability to verbally estimate numbers of items without counting. How does the quality of the mapping between approximate and exact numbers relate to children's math abilities? The role of the ANS-number word mapping in math competence remains controversial for at least two reasons. First, previous work has not examined the relation between verbal estimation and distinct subtypes of math abilities. Second, previous work has not addressed how distinct components of verbal estimation-mapping accuracy and variability-might each relate to math performance. Here, we addressed these gaps by measuring individual differences in ANS precision, verbal number estimation, and formal and informal math abilities in 5- to 7-year-old children. We found that verbal estimation variability, but not estimation accuracy, predicted formal math abilities, even when controlling for age, expressive vocabulary, and ANS precision, and that it mediated the link between ANS precision and overall math ability. These findings suggest that variability in the ANS-number word mapping may be especially important for formal math abilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Nanofluid slip flow over a stretching cylinder with Schmidt and Péclet number effects

NASA Astrophysics Data System (ADS)

Md Basir, Md Faisal; Uddin, M. J.; Md. Ismail, A. I.; Bég, O. Anwar

2016-05-01

A mathematical model is presented for three-dimensional unsteady boundary layer slip flow of Newtonian nanofluids containing gyrotactic microorganisms over a stretching cylinder. Both hydrodynamic and thermal slips are included. By applying suitable similarity transformations, the governing equations are transformed into a set of nonlinear ordinary differential equations with appropriate boundary conditions. The transformed nonlinear ordinary differential boundary value problem is then solved using the Runge-Kutta-Fehlberg fourth-fifth order numerical method in Maple 18 symbolic software. The effects of the controlling parameters on the dimensionless velocity, temperature, nanoparticle volume fractions and microorganism motile density functions have been illustrated graphically. Comparisons of the present paper with the existing published results indicate good agreement and supports the validity and the accuracy of our numerical computations. Increasing bioconvection Schmidt number is observed to depress motile micro-organism density function. Increasing thermal slip parameter leads to a decrease in temperature. Thermal slip also exerts a strong influence on nano-particle concentration. The flow is accelerated with positive unsteadiness parameter (accelerating cylinder) and temperature and micro-organism density function are also increased. However nano-particle concentration is reduced with positive unsteadiness parameter. Increasing hydrodynamic slip is observed to boost temperatures and micro-organism density whereas it decelerates the flow and reduces nano-particle concentrations. The study is relevant to nano-biopolymer manufacturing processes.

Rotation number of integrable symplectic mappings of the plane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zolkin, Timofey; Nagaitsev, Sergei; Danilov, Viatcheslav

2017-04-11

Symplectic mappings are discrete-time analogs of Hamiltonian systems. They appear in many areas of physics, including, for example, accelerators, plasma, and fluids. Integrable mappings, a subclass of symplectic mappings, are equivalent to a Twist map, with a rotation number, constant along the phase trajectory. In this letter, we propose a succinct expression to determine the rotation number and present two examples. Similar to the period of the bounded motion in Hamiltonian systems, the rotation number is the most fundamental property of integrable maps and it provides a way to analyze the phase-space dynamics.

Hydrodynamics of pedestrians' instability in floodwaters

NASA Astrophysics Data System (ADS)

Arrighi, Chiara; Oumeraci, Hocine; Castelli, Fabio

2017-01-01

People's safety is the first objective to be fulfilled by flood risk mitigation measures, and according to existing reports on the causes of casualties, most of the fatalities are due to inappropriate behaviour such as walking or driving in floodwaters. Currently available experimental data on people instability in floodwaters suffer from a large dispersion primarily depending on the large variability of the physical characteristics of the subjects. This paper introduces a dimensionless mobility parameter θP for people partly immersed in flood flows, which accounts for both flood and subject characteristics. The parameter θP is capable of identifying a unique threshold of instability depending on a Froude number, thus reducing the scatter of existing experimental data. Moreover, a three-dimensional (3-D) numerical model describing the detailed geometry of a human body and reproducing a selection of critical pairs of water depth and velocity is presented. The numerical results in terms of hydrodynamic forces and force coefficients are analysed and discussed. Both the mobility parameter θP and the numerical results hint at the crucial role of the Froude number and relative submergence as the most relevant dimensionless numbers to interpret the loss of stability. Finally, the mobility parameter θP is compared with an analogous dimensionless parameter for vehicles' instability in floodwaters, providing a new contribution to support flood risk management and educating people.

MHD Free Convective Boundary Layer Flow of a Nanofluid past a Flat Vertical Plate with Newtonian Heating Boundary Condition

PubMed Central

Uddin, Mohammed J.; Khan, Waqar A.; Ismail, Ahmed I.

2012-01-01

Steady two dimensional MHD laminar free convective boundary layer flows of an electrically conducting Newtonian nanofluid over a solid stationary vertical plate in a quiescent fluid taking into account the Newtonian heating boundary condition is investigated numerically. A magnetic field can be used to control the motion of an electrically conducting fluid in micro/nano scale systems used for transportation of fluid. The transport equations along with the boundary conditions are first converted into dimensionless form and then using linear group of transformations, the similarity governing equations are developed. The transformed equations are solved numerically using the Runge-Kutta-Fehlberg fourth-fifth order method with shooting technique. The effects of different controlling parameters, namely, Lewis number, Prandtl number, buoyancy ratio, thermophoresis, Brownian motion, magnetic field and Newtonian heating on the flow and heat transfer are investigated. The numerical results for the dimensionless axial velocity, temperature and nanoparticle volume fraction as well as the reduced Nusselt and Sherwood number have been presented graphically and discussed. It is found that the rate of heat and mass transfer increase as Newtonian heating parameter increases. The dimensionless velocity and temperature distributions increase with the increase of Newtonian heating parameter. The results of the reduced heat transfer rate is compared for convective heating boundary condition and found an excellent agreement. PMID:23166688

Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors.

PubMed

Martin-Trujillo, Alex; Vidal, Enrique; Monteagudo-Sa Nchez, Ana; Sanchez-Delgado, Marta; Moran, Sebastian; Hernandez Mora, Jose Ramon; Heyn, Holger; Guitart, Miriam; Esteller, Manel; Monk, David

2017-09-07

It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.

DNA Copy Number Signature to Predict Recurrence in Early Stage Ovarian Cancer

DTIC Science & Technology

2016-08-01

AWARD NUMBER: W81XWH-14-1-0194 TITLE: DNA Copy Number Signature to Predict Recurrence in Early-Stage Ovarian Cancer PRINCIPAL INVESTIGATOR...SUBTITLE 5a. CONTRACT NUMBER DNA Copy Number Signature to Predict Recurrence in Early-Stage Ovarian Cancer 5b. GRANT NUMBER W81XWH-14-1-0194 5c. PROGRAM...determine the copy number gain and loss for early stage high grade ovarian cancers through IlluminaHumanOmniExpress-FFPE BeadChip system • Subtask 1 DNA

General statistics of stochastic process of gene expression in eukaryotic cells.

PubMed Central

Kuznetsov, V A; Knott, G D; Bonner, R F

2002-01-01

Thousands of genes are expressed at such very low levels (< or =1 copy per cell) that global gene expression analysis of rarer transcripts remains problematic. Ambiguity in identification of rarer transcripts creates considerable uncertainty in fundamental questions such as the total number of genes expressed in an organism and the biological significance of rarer transcripts. Knowing the distribution of the true number of genes expressed at each level and the corresponding gene expression level probability function (GELPF) could help resolve these uncertainties. We found that all observed large-scale gene expression data sets in yeast, mouse, and human cells follow a Pareto-like distribution model skewed by many low-abundance transcripts. A novel stochastic model of the gene expression process predicts the universality of the GELPF both across different cell types within a multicellular organism and across different organisms. This model allows us to predict the frequency distribution of all gene expression levels within a single cell and to estimate the number of expressed genes in a single cell and in a population of cells. A random "basal" transcription mechanism for protein-coding genes in all or almost all eukaryotic cell types is predicted. This fundamental mechanism might enhance the expression of rarely expressed genes and, thus, provide a basic level of phenotypic diversity, adaptability, and random monoallelic expression in cell populations. PMID:12136033

Determination of absolute expression profiles using multiplexed miRNA analysis

PubMed Central

Song, Jee Hoon; Cheng, Yulan; Saeui, Christopher T.; Cheung, Douglas G.; Croce, Carlo M.; Yarema, Kevin J.; Meltzer, Stephen J.; Liu, Kelvin J.; Wang, Tza-Huei

2017-01-01

Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR’s ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes. PMID:28704432

Dynamic Stiffness and Damping Characteristics of a High-Temperature Air Foil Journal Bearing

NASA Technical Reports Server (NTRS)

Howard, Samuel A.; DellaCorte, Christopher; Valco, Mark J.; Prahl, Joseph M.; Heshmat, Hooshang

2001-01-01

Using a high-temperature optically based displacement measurement system, a foil air bearing's stiffness and damping characteristics were experimentally determined. Results were obtained over a range of modified Sommerfeld Number from 1.5E6 to 1.5E7, and at temperatures from 25 to 538 C. An Experimental procedure was developed comparing the error in two curve fitting functions to reveal different modes of physical behavior throughout the operating domain. The maximum change in dimensionless stiffness was 3.0E-2 to 6.5E-2 over the Sommerfeld Number range tested. Stiffness decreased with temperature by as much as a factor of two from 25 to 538 C. Dimensionless damping was a stronger function of Sommerfeld Number ranging from 20 to 300. The temperature effect on damping being more qualitative, showed the damping mechanism shifted from viscous type damping to frictional type as temperature increased.

High-throughput Cloning and Expression of Integral Membrane Proteins in Escherichia coli

PubMed Central

Bruni, Renato

2014-01-01

Recently, several structural genomics centers have been established and a remarkable number of three-dimensional structures of soluble proteins have been solved. For membrane proteins, the number of structures solved has been significantly trailing those for their soluble counterparts, not least because over-expression and purification of membrane proteins is a much more arduous process. By using high throughput technologies, a large number of membrane protein targets can be screened simultaneously and a greater number of expression and purification conditions can be employed, leading to a higher probability of successfully determining the structure of membrane proteins. This unit describes the cloning, expression and screening of membrane proteins using high throughput methodologies developed in our laboratory. Basic Protocol 1 deals with the cloning of inserts into expression vectors by ligation-independent cloning. Basic Protocol 2 describes the expression and purification of the target proteins on a miniscale. Lastly, for the targets that express at the miniscale, basic protocols 3 and 4 outline the methods employed for the expression and purification of targets at the midi-scale, as well as a procedure for detergent screening and identification of detergent(s) in which the target protein is stable. PMID:24510647

Regional analysis of annual precipitation maxima in Montana

USGS Publications Warehouse

Parrett, Charles

1997-01-01

Dimensionless precipitation-frequency curves for estimating precipitation depths having large recurrence intervals were developed for 2-, 6-, and 24-hour storm durations for three homogeneous regions in Montana. Within each homogeneous region, at-site annual precipitation maxima were made dimensionless by dividing by the at-site mean and grouped so that a single frequency curve would be applicable for each duration. L-moment statistics were used to help define the homogeneous regions and to develop the dimensionless precipitation- frequency curves. Data from 459 precipitation stations were used after application of statistical tests to ensure that the data were not serially correlated and were stationary over the general period of data collection (1900-92). The data were found to have a small, but significant, degree of interstation correlation. The GEV distribution was used to construct dimensionless frequency curves of annual precipitation maxima for each duration within each region. Each dimensionless frequency curve was considered to be reliable for recurrence intervals up to the effective record length. Because of significant, though small, interstation correlation in all regions for all durations, and because the selected regions exhibited some heterogeneity, the effective record length was considered to be less than the total number of station-years of data. The effective record length for each duration in each region was estimated using a graphical method and found to range from 500 years for 6-hour duration data in Region 2 to 5,100 years for 24-hour duration data in Region 3.

Comment on ‘On the units radian and cycle for the quantity plane angle’

NASA Astrophysics Data System (ADS)

Leonard, B. P.

2016-12-01

In the referenced paper, Ian Mills addresses the confusion caused by the treatment of plane angle in the International System of Units (SI). As he points out, what the SI calls an ‘angle’ is not a dimensional physical quantity but, rather, the dimensionless numerical value of the angle when expressed in radians, thus creating widespread confusion regarding terminology and notation. For example, Mills shows that for the harmonic oscillator, if the conventional argument of the sinusoid represents an angle, it must be divided by a dimensional constant equal to one radian in order to correctly render it dimensionless, thereby greatly clarifying the notation. However, there is a problem with the author’s interpretation of frequency. Although, for uniform rotation, Mills correctly defines the revolution frequency as the number of complete revolutions, N, divided by the time interval, he takes the unit for N to be ‘cycle’ (which he defines as one revolution) rather than the correct unit: the number one. The unit for ‘frequency’ then appears to be ‘cycle per second’ (i.e. revolution per second), whereas it should be one per second, correctly called hertz. Thus Mills concludes that ‘frequency’ is the same physical quantity as angular velocity and calls for the ‘hertz’ to be redefined as 2π rad s-1, a non-coherent derived unit for angular velocity. This misinterpretation of frequency corrupts the remainder of the author’s discussion of the examples considered. In my comment, I explain and correct these and related errors.

Mutant number distribution in an exponentially growing population

NASA Astrophysics Data System (ADS)

Keller, Peter; Antal, Tibor

2015-01-01

We present an explicit solution to a classic model of cell-population growth introduced by Luria and Delbrück (1943 Genetics 28 491-511) 70 years ago to study the emergence of mutations in bacterial populations. In this model a wild-type population is assumed to grow exponentially in a deterministic fashion. Proportional to the wild-type population size, mutants arrive randomly and initiate new sub-populations of mutants that grow stochastically according to a supercritical birth and death process. We give an exact expression for the generating function of the total number of mutants at a given wild-type population size. We present a simple expression for the probability of finding no mutants, and a recursion formula for the probability of finding a given number of mutants. In the ‘large population-small mutation’ limit we recover recent results of Kessler and Levine (2014 J. Stat. Phys. doi:10.1007/s10955-014-1143-3) for a fully stochastic version of the process.

A minimalist probabilistic description of root zone soil water

USGS Publications Warehouse

Milly, P.C.D.

2001-01-01

The probabilistic response of depth‐integrated soil water to given climatic forcing can be described readily using an existing supply‐demand‐storage model. An apparently complex interaction of numerous soil, climate, and plant controls can be reduced to a relatively simple expression for the equilibrium probability density function of soil water as a function of only two dimensionless parameters. These are the index of dryness (ratio of mean potential evaporation to mean precipitation) and a dimensionless storage capacity (active root zone soil water capacity divided by mean storm depth). The first parameter is mainly controlled by climate, with surface albedo playing a subsidiary role in determining net radiation. The second is a composite of soil (through moisture retention characteristics), vegetation (through rooting characteristics), and climate (mean storm depth). This minimalist analysis captures many essential features of a more general probabilistic analysis, but with a considerable reduction in complexity and consequent elucidation of the critical controls on soil water variability. In particular, it is shown that (1) the dependence of mean soil water on the index of dryness approaches a step function in the limit of large soil water capacity; (2) soil water variance is usually maximized when the index of dryness equals 1, and the width of the peak varies inversely with dimensionless storage capacity; (3) soil water has a uniform probability density function when the index of dryness is 1 and the dimensionless storage capacity is large; and (4) the soil water probability density function is bimodal if and only if the index of dryness is <1, but this bimodality is pronounced only for artificially small values of the dimensionless storage capacity.

Experimental study of laser-oxygen cutting of low-carbon steel using fibre and CO{sub 2} lasers under conditions of minimal roughness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Golyshev, A A; Malikov, A G; Orishich, A M

The results of an experimental study of laser-oxygen cutting of low-carbon steel using fibre and CO{sub 2} lasers are generalised. The dependence of roughness of the cut surface on the cutting parameters is investigated, and the conditions under which the surface roughness is minimal are formulated. It is shown that for both types of lasers these conditions can be expressed in the same way in terms of the dimensionless variables – the Péclet number Pe and the output power Q of laser radiation per unit thickness of the cut sheet – and take the form of the similarity laws: Pemore » = const, Q = const. The optimal values of Pe and Q are found. We have derived empirical expressions that relate the laser power and cutting speed with the thickness of the cut sheet under the condition of minimal roughness in the case of cutting by means of radiation from fibre and CO{sub 2} lasers. (laser technologies)« less

Development of Dimensionless Surge Response Functions for Hazard Assessment at Panama City, Florida

NASA Astrophysics Data System (ADS)

Taylor, N. R.; Irish, J. L.; Hagen, S. C.; Kaihatu, J. M.; McLaughlin, P. W.

2013-12-01

Reliable and robust methods of extreme value analysis in hurricane surge forecasting are of high importance in the coastal engineering profession. The Joint Probability Method (JPM) has become the preferred statistical method over the Historical Surge Population (HSP) method, due to its ability to give more accurate surge predictions, as demonstrated by Irish et. al in 2011 (J. Geophys. Res.). One disadvantage to this method is its high computational cost; a single location can require hundreds of simulated storms, each needing one thousand computational hours or more to complete. One way of overcoming this issue is to use an interpolating function, called a surge response function, to reduce the required number of simulations to a manageable number. These sampling methods, which use physical scaling laws, have been shown to significantly reduce the number of simulated storms needed for application of the JPM method. In 2008, Irish et. al. (J. Phys. Oceanogr.) demonstrated that hurricane surge scales primarily as a function of storm size and intensity. Additionally, Song et. al. in 2012 (Nat. Hazards) has shown that surge response functions incorporating bathymetric variations yield highly accurate surge estimates along the Texas coastline. This study applies the Song. et. al. model to 73 stations along the open coast, and 273 stations within the bays, in Panama City, Florida. The model performs well for the open coast and bay areas; surge levels at most stations along the open coast were predicted with RMS errors below 0.40 meters, and R2 values at or above 0.80. The R2 values for surge response functions within bays were consistently at or above 0.75. Surge levels at most stations within the North Bay and East Bay were predicted with RMS errors below 0.40 meters; within the West Bay, surge was predicted with RMS errors below 0.52 meters. Accurately interpolating surge values along the Panama City coast and bays enables efficient use of the JPM model in order to

The Precision of Mapping Between Number Words and the Approximate Number System Predicts Children’s Formal Math Abilities

PubMed Central

Libertus, Melissa E.; Odic, Darko; Feigenson, Lisa; Halberda, Justin

2016-01-01

Children can represent number in at least two ways: by using their non-verbal, intuitive Approximate Number System (ANS), and by using words and symbols to count and represent numbers exactly. Further, by the time they are five years old, children can map between the ANS and number words, as evidenced by their ability to verbally estimate numbers of items without counting. How does the quality of the mapping between approximate and exact numbers relate to children’s math abilities? The role of the ANS-number word mapping in math competence remains controversial for at least two reasons. First, previous work has not examined the relation between verbal estimation and distinct subtypes of math abilities. Second, previous work has not addressed how distinct components of verbal estimation – mapping accuracy and variability – might each relate to math performance. Here, we address these gaps by measuring individual differences in ANS precision, verbal number estimation, and formal and informal math abilities in 5- to 7-year-old children. We found that verbal estimation variability, but not estimation accuracy, predicted formal math abilities even when controlling for age, expressive vocabulary, and ANS precision, and that it mediated the link between ANS precision and overall math ability. These findings suggest that variability in the ANS-number word mapping may be especially important for formal math abilities. PMID:27348475

A mechanism of thrust enhancement on a heaving plate due to flexibility at moderately low Reynolds numbers

NASA Astrophysics Data System (ADS)

Lin, Yung-Sheng; Tzeng, Yau-Ting; Chang, Chien-Cheng; Chu, Chin-Chou

2017-11-01

A numerical study is conducted to investigate the force mechanisms for a 3D heaving flexible plate from the perspective of a diagnostic force element analysis (Chang 1992). The problem is relevant to a simplified flapping fish-tail with the front edge held fixed in space. The flow is assumed to be laminar with the Reynolds numbers fixed at Re =200 or 500, and the Strouhal number St ranging from 0.1 to 0.6, and the flexure amplitude of the plate a0 for 0.1 to 0.25 (dimensionless). It is shown that heaving, whilst increasing thrust generation, also reduces the frictional drag, yet the flexibility promotes thrust generation at the expense of accruing more frictional drag. In the literature, the thrust exerted on the tail-mimicking plate is largely credited to the vortices in the wake. However, this study performs a regional force analysis to show that the vorticity in the wake region supplies approximately 20-30% of the total thrust, especially in the cases of strong thrust generation. Comparable contributions come also from the regions direct above and below the heaving plate (mainly including the attached vortices) as well as from the two side regions (mainly including the tip vortices) next to the flapping plate. In addition, the potential motion associated with the unsteady flapping and the contribution from the surface vorticity are non-negligible constituent force components. MOST, TAIWAN under Contacts NO. 105-2221-E-002-097-MY3 and NO. 105-2221-E-002 -105 -MY3.

Mathematical Models and Calculation of the Coefficients of Heat and Mass Transfer in the Packings of Mechanical-Draft Towers

NASA Astrophysics Data System (ADS)

Laptev, A. G.; Lapteva, E. A.

2017-05-01

Semiempirical expressions for calculating the average coefficients of heat and mass transfer in the blocks of film-type sprayers are considered. The equations of the Chilton-Colburn hydrodynamic analogy, Prandtl model, generalizations of the hydrodynamic analogy, as well as dimensionless expressions and experimental data of various authors have been used. It is shown that the best agreement with experiment is provided by equations obtained with the aid of the hydrodynamic analogy and Prandtl model.

Role of Rayleigh numbers on characteristics of double diffusive salt fingers

NASA Astrophysics Data System (ADS)

Rehman, F.; Singh, O. P.

2018-05-01

Double diffusion convection, driven by two constituents of the fluid with different molecular diffusivity, is widely applied in oceanography and large number of other fields like astrophysics, geology, chemistry and metallurgy. In case of ocean, heat (T) and salinity (S) are the two components with varying diffusivity, where heat diffuses hundred times faster than salt. Component (T) stabilizes the system whereas components (S) destabilizes the system with overall density remains stable and forms the rising and sinking fingers known as salt fingers. Recent observations suggest that salt finger characteristics such as growth rates, wavenumber, and fluxes are strongly depending on the Rayleigh numbers as major driving force. In this paper, we corroborate this observation with the help of experiments, numerical simulations and linear theory. An eigenvalue expression for growth rate is derived from the linearized governing equations with explicit dependence on Rayleigh numbers, density stability ratio, Prandtl number and diffusivity ratio. Expressions for fastest growing fingers are also derived as a function various non-dimensional parameter. The predicted results corroborate well with the data reported from the field measurements, experiments and numerical simulations.

Film thickness for different regimes of fluid-film lubrication. [elliptical contacts

NASA Technical Reports Server (NTRS)

Hamrock, B. J.; Dowson, D.

1983-01-01

Mathematical formulas are presented which express the dimensionless minimum film thickness for the four lubrication regimes found in elliptical contacts: isoviscous-rigid regime; piezoviscous-rigid regime; isoviscous-elastic regime; and piezoviscous-elastic regime. The relative importance of pressure on elastic distortion and lubricant viscosity is the factor that distinguishes these regimes for a given conjunction geometry. In addition, these equations were used to develop maps of the lubrication regimes by plotting film thickness contours on a log-log grid of the dimensionless viscosity and elasticity parameters for three values of the ellipticity parameter. These results present a complete theoretical film thickness parameter solution for elliptical constants in the four lubrication regimes. The results are particularly useful in initial investigations of many practical lubrication problems involving elliptical conjunctions.

Processing Idiomatic Expressions: Effects of Semantic Compositionality

ERIC Educational Resources Information Center

Tabossi, Patrizia; Fanari, Rachele; Wolf, Kinou

2008-01-01

Three experiments tested the main claims of the idiom decomposition hypothesis: People have clear intuitions on the semantic compositionality of idiomatic expressions, which determines the syntactic behavior of these expressions and how they are recognized. Experiment 1 showed that intuitions are clear only for a very restricted number of…

Expected Number of Passes in a Binary Search Scheme

ERIC Educational Resources Information Center

Tenenbein, Aaron

1974-01-01

The binary search scheme is a method of finding a particular file from a set of ordered files stored in a computer. In this article an exact expression for the expected number of passes required to find a file is derived. (Author)

Investigating the Variability in Cumulus Cloud Number as a Function of Subdomain Size and Organization using large-domain LES

NASA Astrophysics Data System (ADS)

Neggers, R.

2017-12-01

Recent advances in supercomputing have introduced a "grey zone" in the representation of cumulus convection in general circulation models, in which this process is partially resolved. Cumulus parameterizations need to be made scale-aware and scale-adaptive to be able to conceptually and practically deal with this situation. A potential way forward are schemes formulated in terms of discretized Cloud Size Densities, or CSDs. Advantages include i) the introduction of scale-awareness at the foundation of the scheme, and ii) the possibility to apply size-filtering of parameterized convective transport and clouds. The CSD is a new variable that requires closure; this concerns its shape, its range, but also variability in cloud number that can appear due to i) subsampling effects and ii) organization in a cloud field. The goal of this study is to gain insight by means of sub-domain analyses of various large-domain LES realizations of cumulus cloud populations. For a series of three-dimensional snapshots, each with a different degree of organization, the cloud size distribution is calculated in all subdomains, for a range of subdomain sizes. The standard deviation of the number of clouds of a certain size is found to decrease with the subdomain size, following a powerlaw scaling corresponding to an inverse-linear dependence. Cloud number variability also increases with cloud size; this reflects that subsampling affects the largest clouds first, due to their typically larger neighbor spacing. Rewriting this dependence in terms of two dimensionless groups, by dividing by cloud number and cloud size respectively, yields a data collapse. Organization in the cloud field is found to act on top of this primary dependence, by enhancing the cloud number variability at the smaller sizes. This behavior reflects that small clouds start to "live" on top of larger structures such as cold pools, favoring or inhibiting their formation (as illustrated by the attached figure of cloud mask

Levels of duplicate gene expression in armoured catfishes.

PubMed

Dunham, R A; Philipp, D P; Whitt, G S

1980-01-01

Species of armoured catfishes differ significantly in their cellular DNA content and chromosome number. Starch gel electrophoresis of isozymes was used to determine whether each of 16 enzyme loci was expressed in a single or duplicate state. The percent of enzyme loci exhibiting duplicate locus expression in Corydoras aeneus, Corydoras julii, Corydoras melanistius, and Corydoras myersi was 37.5 percent, 18.75 percent, 12.5 percent, and 6.25 percent, respectively. The percentage of loci expressed in duplicate is higher in the species with higher haploid DNA contents, which are 4.4 pg, 3.0 pg, and 2.3 pg, respectively. These differences in DNA contents are also associated with differences in chromosome number. These data are consistent with the hypothesis that increases in DNA contents and enzyme loci occur both by tetraploidization and by regional gene duplication and that these increases are then followed by a partial loss of DNA and a reduction in the number of the duplicate isozyme loci expressed. Such analyses provide insight into the mechanisms of genome amplification and reduction as well as insights into the fats of duplicate genes.

Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

PubMed Central

Camps, Jordi; Nguyen, Quang Tri; Padilla-Nash, Hesed M.; Knutsen, Turid; McNeil, Nicole E.; Wangsa, Danny; Hummon, Amanda B.; Grade, Marian; Ried, Thomas; Difilippantonio, Michael J.

2016-01-01

To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations. PMID:19691111

Personality expression in Chinese language use.

PubMed

Qiu, Lin; Lu, Jiahui; Ramsay, Jonathan; Yang, Shanshan; Qu, Weina; Zhu, Tingshao

2017-12-01

To date, little research has investigated personality expressions in languages other than English. Given that the Chinese language has the largest number of native speakers in the world, it is vitally important to examine the associations between personality and Chinese language use. In this research, we analysed Chinese microblogs and identified word categories and factorial structures associated with personality traits. We also compared our results with previous findings in English and showed that linguistic expression of personality has both universal- and language-specific aspects. Expression of personality via content words is more likely to be consistent across languages than expression via function words. This makes an important step towards uncovering universal patterns of personality expression in language. © 2016 International Union of Psychological Science.

Altered JS-2 expression in colorectal cancers and its clinical pathological relevance.

PubMed

Lam, Alfred King-Yin; Gopalan, Vinod; Nassiri, Mohammad Reza; Kasim, Kais; Dissanayake, Jayampathy; Tang, Johnny Chuek-On; Smith, Robert Anthony

2011-10-01

JS-2 is a novel gene located at 5p15.2 and originally detected in primary oesophageal cancer. There is no study on the role of JS-2 in colorectal cancer. The aim of this study is to determine the gene copy number and expression of JS-2 in a large cohort of patients with colorectal tumours and correlate these to the clinicopathological features of the cancer patients. We evaluated the DNA copy number and mRNA expression of JS-2 in 176 colorectal tissues (116 adenocarcinomas, 30 adenomas and 30 non-neoplastic tissues) using real-time polymerase chain reaction. JS-2 expression was also evaluated in two colorectal cancer cell lines and a benign colorectal cell line. JS-2 amplification was noted in 35% of the colorectal adenocarcinomas. Significant differences in relative expression levels for JS-2 mRNA between different colorectal tissues were noted (p = 0.05). Distal colorectal adenocarcinoma had significantly higher copy number than proximal adenocarcinoma (p = 0.005). The relative expression level of JS-2 was different between colonic and rectal adenocarcinoma (p = 0.007). Mucinous adenocarcinoma showed higher JS-2 expression than non-mucinous adenocarcinoma (p = 0.02). Early T-stage cancers appear to have higher JS-2 copy number and lower expression of JS-2 mRNA than later stage cancers (p = 0.001 and 0.03 respectively). Colorectal cancer cell lines showed lower expression of JS-2 than the benign colorectal cell line. JS-2 copy number change and expression were shown for the first time to be altered in the carcinogenesis of colorectal cancer. In addition, genetic alteration of JS-2 was found to be related to location, pathological subtypes and staging of colorectal cancer. Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Instability and associated roll structure of Marangoni convection in high Prandtl number liquid bridge with large aspect ratio

NASA Astrophysics Data System (ADS)

Yano, T.; Nishino, K.; Kawamura, H.; Ueno, I.; Matsumoto, S.

2015-02-01

This paper reports the experimental results on the instability and associated roll structures (RSs) of Marangoni convection in liquid bridges formed under the microgravity environment on the International Space Station. The geometry of interest is high aspect ratio (AR = height/diameter ≥ 1.0) liquid bridges of high Prandtl number fluids (Pr = 67 and 207) suspended between coaxial disks heated differentially. The unsteady flow field and associated RSs were revealed with the three-dimensional particle tracking velocimetry. It is found that the flow field after the onset of instability exhibits oscillations with azimuthal mode number m = 1 and associated RSs traveling in the axial direction. The RSs travel in the same direction as the surface flow (co-flow direction) for 1.00 ≤ AR ≤ 1.25 while they travel in the opposite direction (counter-flow direction) for AR ≥ 1.50, thus showing the change of traveling directions with AR. This traveling direction for AR ≥ 1.50 is reversed to the co-flow direction when the temperature difference between the disks is increased to the condition far beyond the critical one. This change of traveling directions is accompanied by the increase of the oscillation frequency. The characteristics of the RSs for AR ≥ 1.50, such as the azimuthal mode of oscillation, the dimensionless oscillation frequency, and the traveling direction, are in reasonable agreement with those of the previous sounding rocket experiment for AR = 2.50 and those of the linear stability analysis of an infinite liquid bridge.

Permeable disks at low Reynolds numbers

NASA Astrophysics Data System (ADS)

Viola, Ignazio Maria; Cummins, Cathal; Mastropaolo, Enrico; Nakayama, Naomi

2017-11-01

The wake of a permeable disk can be rather exceptional: a toroidal vortex can form and remains stably at a fixed distance from the disk. The streamwise length of the vortex depends on the Reynolds and Darcy numbers. We investigate this fascinating flow for Reynolds numbers from 10 to 130 and Darcy numbers (Da) from 10-9 to 1. Direct numerical simulations are performed on a 2D grid with axisymmetric boundary conditions. Three flow regimes are observed: for low Da (effectively impervious), the wake is characterized by the presence of a toroidal vortex whose length is approximately equal to that of an impervious disk. For 10-6 < Da <10-3 , the increase in Da causes the vortex to shorten, and eventually vanishes at a critical Darcy number. It is demonstrated that increasing the permeability can lead to large variations in the length of the recirculating wake but with minimal effect on the drag coefficient. For higher Da (highly permeable), there is no recirculation, and an analytical expression for the drag force on the disk is derived, showing good agreement with the numerical results. This work was supported by the Leverhulme Trust [RPG-2015-255].

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes.

PubMed

Boivin, Vincent; Deschamps-Francoeur, Gabrielle; Couture, Sonia; Nottingham, Ryan M; Bouchard-Bourelle, Philia; Lambowitz, Alan M; Scott, Michelle S; Abou-Elela, Sherif

2018-07-01

Comparing the abundance of one RNA molecule to another is crucial for understanding cellular functions but most sequencing techniques can target only specific subsets of RNA. In this study, we used a new fragmented ribodepleted TGIRT sequencing method that uses a thermostable group II intron reverse transcriptase (TGIRT) to generate a portrait of the human transcriptome depicting the quantitative relationship of all classes of nonribosomal RNA longer than 60 nt. Comparison between different sequencing methods indicated that FRT is more accurate in ranking both mRNA and noncoding RNA than viral reverse transcriptase-based sequencing methods, even those that specifically target these species. Measurements of RNA abundance in different cell lines using this method correlate with biochemical estimates, confirming tRNA as the most abundant nonribosomal RNA biotype. However, the single most abundant transcript is 7SL RNA, a component of the signal recognition particle. S tructured n on c oding RNAs (sncRNAs) associated with the same biological process are expressed at similar levels, with the exception of RNAs with multiple functions like U1 snRNA. In general, sncRNAs forming RNPs are hundreds to thousands of times more abundant than their mRNA counterparts. Surprisingly, only 50 sncRNA genes produce half of the non-rRNA transcripts detected in two different cell lines. Together the results indicate that the human transcriptome is dominated by a small number of highly expressed sncRNAs specializing in functions related to translation and splicing. © 2018 Boivin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Frequency Dependent Macro-dispersion Induced by Oscillatory Inputs and Spatial Heterogeneity

NASA Astrophysics Data System (ADS)

Rajabi, F.; Battiato, I.

2017-12-01

Elucidating flow and transport processes at the pore scale is the cornerstone of most hydrologic studies in the subsurface. This becomes even more imperative when the system is subject to a cyclic forcing. Such temporal variations with evolving heterogeneity of time scales spanning from days to years can influence transport phenomena at the pore level, e.g. yearly freeze/thaw in the thin active layer of soil above permafrost zone whose thickness increases throughout the thaw season. Moreover, understanding the interactions of different physical phenomena at the pore scale is key to predict the behavior at the continuum scale. Yet, the connection between periodic inputs at the pore scale and macrotransport is to a great extent unknown. In the spirit of homogenization technique, we derived a macrotime continuum-scale equation as well as expressions for the effective transport coefficients. The macrodispersion arises from contributions of molecular diffusion, spatial heterogeneity and time-dependent fluctuations. Moreover, we have quantified the solute spreading by effective dispersion in terms of dimensionless numbers (Pe, Da, and Strouhal), i.e. expressing the interplay of molecular diffusion, advection, reaction and signal frequency. Yet, as every macroscopic model, spatiotemporally averaged models can breakdown when certain criteria are violated. This makes the continuum scale equation a poor approximation for the processes at the pore scale. To this end, we also provide the conditions under which the space-time averaged equations accurately describe pore-scale processes. In addition, this study gives a robust evidence that transverse mixing can in fact benefit from fluctuating boundary forcing due to the interaction of temporal fluctuations and molecular diffusion. Furthermore, it provides a robust quantitative foundation for designing the desired systems since the interplay of geometry and external forcing has been directly connected to each other in terms of

Monoallelic Gene Expression in Mammals.

PubMed

Chess, Andrew

2016-11-23

Monoallelic expression not due to cis-regulatory sequence polymorphism poses an intriguing problem in epigenetics because it requires the unequal treatment of two segments of DNA that are present in the same nucleus and that can indeed have absolutely identical sequences. Here, I focus on a few recent developments in the field of monoallelic expression that are of particular interest and raise interesting questions for future work. One development is regarding analyses of imprinted genes, in which recent work suggests the possibility that intriguing networks of imprinted genes exist and are important for genetic and physiological studies. Another issue that has been raised in recent years by a number of publications is the question of how skewed allelic expression should be for it to be designated as monoallelic expression and, further, what methods are appropriate or inappropriate for analyzing genomic data to examine allele-specific expression. Perhaps the most exciting recent development in mammalian monoallelic expression is a clever and carefully executed analysis of genetic diversity of autosomal genes subject to random monoallelic expression (RMAE), which provides compelling evidence for distinct evolutionary forces acting on random monoallelically expressed genes.

Low copy number of the salivary amylase gene predisposes to obesity.

PubMed

Falchi, Mario; El-Sayed Moustafa, Julia Sarah; Takousis, Petros; Pesce, Francesco; Bonnefond, Amélie; Andersson-Assarsson, Johanna C; Sudmant, Peter H; Dorajoo, Rajkumar; Al-Shafai, Mashael Nedham; Bottolo, Leonardo; Ozdemir, Erdal; So, Hon-Cheong; Davies, Robert W; Patrice, Alexandre; Dent, Robert; Mangino, Massimo; Hysi, Pirro G; Dechaume, Aurélie; Huyvaert, Marlène; Skinner, Jane; Pigeyre, Marie; Caiazzo, Robert; Raverdy, Violeta; Vaillant, Emmanuel; Field, Sarah; Balkau, Beverley; Marre, Michel; Visvikis-Siest, Sophie; Weill, Jacques; Poulain-Godefroy, Odile; Jacobson, Peter; Sjostrom, Lars; Hammond, Christopher J; Deloukas, Panos; Sham, Pak Chung; McPherson, Ruth; Lee, Jeannette; Tai, E Shyong; Sladek, Robert; Carlsson, Lena M S; Walley, Andrew; Eichler, Evan E; Pattou, Francois; Spector, Timothy D; Froguel, Philippe

2014-05-01

Common multi-allelic copy number variants (CNVs) appear enriched for phenotypic associations compared to their biallelic counterparts. Here we investigated the influence of gene dosage effects on adiposity through a CNV association study of gene expression levels in adipose tissue. We identified significant association of a multi-allelic CNV encompassing the salivary amylase gene (AMY1) with body mass index (BMI) and obesity, and we replicated this finding in 6,200 subjects. Increased AMY1 copy number was positively associated with both amylase gene expression (P = 2.31 × 10(-14)) and serum enzyme levels (P < 2.20 × 10(-16)), whereas reduced AMY1 copy number was associated with increased BMI (change in BMI per estimated copy = -0.15 (0.02) kg/m(2); P = 6.93 × 10(-10)) and obesity risk (odds ratio (OR) per estimated copy = 1.19, 95% confidence interval (CI) = 1.13-1.26; P = 1.46 × 10(-10)). The OR value of 1.19 per copy of AMY1 translates into about an eightfold difference in risk of obesity between subjects in the top (copy number > 9) and bottom (copy number < 4) 10% of the copy number distribution. Our study provides a first genetic link between carbohydrate metabolism and BMI and demonstrates the power of integrated genomic approaches beyond genome-wide association studies.

Magnetohydrodynamic three-dimensional flow of viscoelastic nanofluid in the presence of nonlinear thermal radiation

NASA Astrophysics Data System (ADS)

Hayat, T.; Muhammad, Taseer; Alsaedi, A.; Alhuthali, M. S.

2015-07-01

Magnetohydrodynamic (MHD) three-dimensional flow of couple stress nanofluid in the presence of thermophoresis and Brownian motion effects is analyzed. Energy equation subject to nonlinear thermal radiation is taken into account. The flow is generated by a bidirectional stretching surface. Fluid is electrically conducting in the presence of a constant applied magnetic field. The induced magnetic field is neglected for a small magnetic Reynolds number. Mathematical formulation is performed using boundary layer analysis. Newly proposed boundary condition requiring zero nanoparticle mass flux is employed. The governing nonlinear mathematical problems are first converted into dimensionless expressions and then solved for the series solutions of velocities, temperature and nanoparticles concentration. Convergence of the constructed solutions is verified. Effects of emerging parameters on the temperature and nanoparticles concentration are plotted and discussed. Skin friction coefficients and Nusselt number are also computed and analyzed. It is found that the thermal boundary layer thickness is an increasing function of radiative effect.

An algorithm for modeling entrainment and naturally and chemically dispersed oil droplet size distribution under surface breaking wave conditions.

PubMed

Li, Zhengkai; Spaulding, Malcolm L; French-McCay, Deborah

2017-06-15

A surface oil entrainment model and droplet size model have been developed to estimate the flux of oil under surface breaking waves. Both equations are expressed in dimensionless Weber number (We) and Ohnesorge number (Oh, which explicitly accounts for the oil viscosity, density, and oil-water interfacial tension). Data from controlled lab studies, large-scale wave tank tests, and field observations have been used to calibrate the constants of the two independent equations. Predictions using the new algorithm compared well with the observed amount of oil removed from the surface and the sizes of the oil droplets entrained in the water column. Simulations with the new algorithm, implemented in a comprehensive spill model, show that entrainment rates increase more rapidly with wind speed than previously predicted based on the existing Delvigne and Sweeney's (1988) model, and a quasi-stable droplet size distribution (d<~50μm) is developed in the near surface water. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influences of AMY1 gene copy number and protein expression on salivary alpha-amylase activity before and after citric acid stimulation in splenic asthenia children.

PubMed

Yang, Zemin; Lin, Jing; Chen, Longhui; Zhang, Min; Yang, Xiaorong; Chen, Weiwen

2015-06-01

To compare the correlations between salivary alpha-amylase (sAA) activity and amylase, alpha 1 (salivary) gene (AMYl) copy number or its gene expression between splenic asthenia and healthy children, and investigate the reasons of attenuated sAA activity ratio before and after citric acid stimulation in splenic asthenia children. Saliva samples from 20 splenic asthenia children and 29 healthy children were collected before and after citric acid stimulation. AMYl copy number, sAA activity, and total sAA and glycosylated sAA contents were determined, and their correlations were analyzed. Although splenic asthenia and healthy children had no differences in AMY1 copy number, splenic asthenia children had positive correlations between AMY1 copy number and sAA activity before or after citric acid stimulation. Splenic asthenia children had a higher sAA glycosylated proportion ratio and glycosylated sAA content ratio, while their total sAA content ratio and sAA activity ratio were lower compared with healthy children. The glycosylated sAA content ratio was higher than the total sAA content ratio in both groups. Splenic asthenia and healthy children had positive correlations between total sAA or glycosylated sAA content and sAA activity. However, the role played by glycosylated sAA content in sAA activity in healthy children increased after citric acid stimulation, while it decreased in splenic asthenia children. Genetic factors like AMY1 copy number variations, and more importantly, sAA glycosylation abnormalities leading to attenuated sAA activity after citric acid stimulation, which were the main reasons of the attenuated sAA activity ratio in splenic asthenia children compared with healthy children.

Stability of stationary inverse transport equation in diffusion scaling

NASA Astrophysics Data System (ADS)

Chen, Ke; Li, Qin; Wang, Li

2018-02-01

We consider the inverse problem of reconstructing the optical parameters for the stationary radiative transfer equation (RTE) from velocity-averaged measurement. The RTE often contains multiple scales, characterized by the magnitude of a dimensionless parameter—the Knudsen number ( \

Degenerate r-Stirling Numbers and r-Bell Polynomials

NASA Astrophysics Data System (ADS)

Kim, T.; Yao, Y.; Kim, D. S.; Jang, G.-W.

2018-01-01

The purpose of this paper is to exploit umbral calculus in order to derive some properties, recurrence relations, and identities related to the degenerate r-Stirling numbers of the second kind and the degenerate r-Bell polynomials. Especially, we will express the degenerate r-Bell polynomials as linear combinations of many well-known families of special polynomials.

Valence, Covalence, Hypervalence, Oxidation State, and Coordination Number

ERIC Educational Resources Information Center

Smith, Derek W.

2005-01-01

Valence as a numerical measure of an atom's combining power, expressed by the number of bonds it forms in a molecular formulation of the compound in question, was unable to cope with coordination compounds. The covalence of an atom is the nearest model equivalent, but is subject to ambiguity since it often depends on which bonding model is being…

Radon-222 as Natural Tracer for Monitoring the Remediation of NAPL Contamination in the Subsurface

DTIC Science & Technology

2008-03-01

aquifer interrogated during the test using: w NAPL S S K1R +== radon tracer V V (3) where R is the retardation factor (dimensionless), Vtracer is...NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR( S ) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME( S ) AND...MONITORING AGENCY NAME( S ) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM( S ) 11. SPONSOR/MONITOR’S REPORT NUMBER( S ) 12. DISTRIBUTION/AVAILABILITY STATEMENT

New similarity of triangular fuzzy number and its application.

PubMed

Zhang, Xixiang; Ma, Weimin; Chen, Liping

2014-01-01

The similarity of triangular fuzzy numbers is an important metric for application of it. There exist several approaches to measure similarity of triangular fuzzy numbers. However, some of them are opt to be large. To make the similarity well distributed, a new method SIAM (Shape's Indifferent Area and Midpoint) to measure triangular fuzzy number is put forward, which takes the shape's indifferent area and midpoint of two triangular fuzzy numbers into consideration. Comparison with other similarity measurements shows the effectiveness of the proposed method. Then, it is applied to collaborative filtering recommendation to measure users' similarity. A collaborative filtering case is used to illustrate users' similarity based on cloud model and triangular fuzzy number; the result indicates that users' similarity based on triangular fuzzy number can obtain better discrimination. Finally, a simulated collaborative filtering recommendation system is developed which uses cloud model and triangular fuzzy number to express users' comprehensive evaluation on items, and result shows that the accuracy of collaborative filtering recommendation based on triangular fuzzy number is higher.

Quantifying the origin of metallic glass formation

NASA Astrophysics Data System (ADS)

Johnson, W. L.; Na, J. H.; Demetriou, M. D.

2016-01-01

The waiting time to form a crystal in a unit volume of homogeneous undercooled liquid exhibits a pronounced minimum τX* at a `nose temperature' T* located between the glass transition temperature Tg, and the crystal melting temperature, TL. Turnbull argued that τX* should increase rapidly with the dimensionless ratio trg=Tg/TL. Angell introduced a dimensionless `fragility parameter', m, to characterize the fall of atomic mobility with temperature above Tg. Both trg and m are widely thought to play a significant role in determining τX*. Here we survey and assess reported data for TL, Tg, trg, m and τX* for a broad range of metallic glasses with widely varying τX*. By analysing this database, we derive a simple empirical expression for τX*(trg, m) that depends exponentially on trg and m, and two fitting parameters. A statistical analysis shows that knowledge of trg and m alone is therefore sufficient to predict τX* within estimated experimental errors. Surprisingly, the liquid/crystal interfacial free energy does not appear in this expression for τX*.

Accurate evaluation for the biofilm-activated sludge reactor using graphical techniques

NASA Astrophysics Data System (ADS)

Fouad, Moharram; Bhargava, Renu

2018-05-01

A complete graphical solution is obtained for the completely mixed biofilm-activated sludge reactor (hybrid reactor). The solution consists of a series of curves deduced from the principal equations of the hybrid system after converting them in dimensionless form. The curves estimate the basic parameters of the hybrid system such as suspended biomass concentration, sludge residence time, wasted mass of sludge, and food to biomass ratio. All of these parameters can be expressed as functions of hydraulic retention time, influent substrate concentration, substrate concentration in the bulk, stagnant liquid layer thickness, and the minimum substrate concentration which can maintain the biofilm growth in addition to the basic kinetics of the activated sludge process in which all these variables are expressed in a dimensionless form. Compared to other solutions of such system these curves are simple, easy to use, and provide an accurate tool for analyzing such system based on fundamental principles. Further, these curves may be used as a quick tool to get the effect of variables change on the other parameters and the whole system.

The role of external and internal mass transfer in the process of Cu2+ removal by natural mineral sorbents.

PubMed

Sljivić, M; Smiciklas, I; Plećas, I; Pejanović, S

2011-07-01

The kinetics of Cu2+ sorption on to zeolite, clay and diatomite was investigated as a function of initial metal concentrations. For consideration of the mass transfer phenomena, single resistance models based on both film and intraparticle diffusion were tested and compared. The obtained results suggested that the rate-limiting step in Cu2+ sorption strongly depended on the sorbent type, as well as on initial cation concentration. The decrease in external mass transfer coefficients with the increase in initial metal concentrations was in excellent agreement with expressions based on Sherwood and Schmidt dimensionless numbers. The internal diffusivities through zeolite particles were in the range 1.0 x 10(-11) to 1.0 x 10(-13) m2/min, depending on the Cu2+ concentration and the applied theoretical model.

Swimming of a sphere in a viscous incompressible fluid with inertia

NASA Astrophysics Data System (ADS)

Felderhof, B. U.; Jones, R. B.

2017-08-01

The swimming of a sphere immersed in a viscous incompressible fluid with inertia is studied for surface modulations of small amplitude on the basis of the Navier-Stokes equations. The mean swimming velocity and the mean rate of dissipation are expressed as quadratic forms in term of the surface displacements. With a choice of a basis set of modes the quadratic forms correspond to two Hermitian matrices. Optimization of the mean swimming velocity for given rate of dissipation requires the solution of a generalized eigenvalue problem involving the two matrices. It is found for surface modulations of low multipole order that the optimal swimming efficiency depends in intricate fashion on a dimensionless scale number involving the radius of the sphere, the period of the cycle, and the kinematic viscosity of the fluid.

Analysis of gas absorption to a thin liquid film in the presence of a zero-order chemical reaction

NASA Technical Reports Server (NTRS)

Rajagopalan, S.; Rahman, M. M.

1995-01-01

The paper presents a detailed theoretical analysis of the process of gas absorption to a thin liquid film adjacent to a horizontal rotating disk. The film is formed by the impingement of a controlled liquid jet at the center of the disk and subsequent radial spreading of liquid along the disk. The chemical reaction between the gas and the liquid film can be expressed as a zero-order homogeneous reaction. The process was modeled by establishing equations for the conservation of mass, momentum, and species concentration and solving them analytically. A scaling analysis was used to determine dominant transport processes. Appropriate boundary conditions were used to solve these equations to develop expressions for the local concentration of gas across the thickness of the film and distributions of film height, bulk concentration, and Sherwood number along the radius of the disk. The partial differential equation for species concentration was solved using the separation of variables technique along with the Duhamel's theorem and the final analytical solution was expressed using confluent hypergeometric functions. Tables for eigenvalues and eigenfunctions are presented for a number of reaction rate constants. A parametric study was performed using Reynolds number, Ekman number, and dimensionless reaction rate as parameters. At all radial locations, Sherwood number increased with Reynolds number (flow rate) as well as Ekman number (rate of rotation). The enhancement of mass transfer due to chemical reaction was found to be small when compared to the case of no reaction (pure absorption), but the enhancement factor was very significant when compared to pure absorption in a stagnant liquid film. The zero-order reaction processes considered in the present investigation included the absorption of oxygen in aqueous alkaline solutions of sodiumdithionite and rhodium complex catalyzed carbonylation of methanol. Present analytical results were compared to previous theoretical

A feeling for the numbers in biology

PubMed Central

Phillips, Rob; Milo, Ron

2009-01-01

Although the quantitative description of biological systems has been going on for centuries, recent advances in the measurement of phenomena ranging from metabolism to gene expression to signal transduction have resulted in a new emphasis on biological numeracy. This article describes the confluence of two different approaches to biological numbers. First, an impressive array of quantitative measurements make it possible to develop intuition about biological numbers ranging from how many gigatons of atmospheric carbon are fixed every year in the process of photosynthesis to the number of membrane transporters needed to provide sugars to rapidly dividing Escherichia coli cells. As a result of the vast array of such quantitative data, the BioNumbers web site has recently been developed as a repository for biology by the numbers. Second, a complementary and powerful tradition of numerical estimates familiar from the physical sciences and canonized in the so-called “Fermi problems” calls for efforts to estimate key biological quantities on the basis of a few foundational facts and simple ideas from physics and chemistry. In this article, we describe these two approaches and illustrate their synergism in several particularly appealing case studies. These case studies reveal the impact that an emphasis on numbers can have on important biological questions. PMID:20018695

Theoretical results for fully flooded, elliptical hydrodynamic contacts

NASA Technical Reports Server (NTRS)

Hamrock, B. J.; Dowson, D.

1982-01-01

The influence of the ellipticity parameter and the dimensionless speed, load, and materials parameters on minimum film thickness was investigated. The ellipticity parameter was varied from 1 (a ball-on-plate configuration) to 8 (a configuration approaching a line contact). The dimensionless speed parameter was varied over a range of nearly two orders of magnitude. Conditions corresponding to the use of solid materials of bronze, steel, and silicon nitride and lubricants of praffinic and naphthemic mineral oils were considered in obtaining the exponent in the dimensionless materials parameter. Thirty-four different cases were used in obtaining the minimum film thickness formula H min = 3.63U to the 0.68 power G to the 0.49 power W to the -0.073 power 1-e to the 0.68K power). A simplified expression for the ellipticity parameter was found where k = 1.03 (r(y)/r(x)) to the 0.64 power. Contour plots were also shown which indicate in detail the pressure spike and two side lobes in which the minimum film thickness occurs. These theoretical solutions of film thickness have all the essential features of the previously reported experimental observations based upon optical interferometry.

Numerical heat transfer study in a scattering, absorbing and emitting semi-transparent porous medium in a cylindrical enclosure

NASA Astrophysics Data System (ADS)

Timoumi, M.; Chérif, B.; Sifaoui, M. S.

2005-12-01

In this paper, heat transfer problem through a semi-transparent porous medium in a cylindrical enclosure is investigated. The governing equations for this problem and the boundary conditions are non-linear differential equations depending on the dimensionless radial coordinate, Planck number N, scattering albedo ω, walls emissivity and thermal conductivity ratio kr. The set of differential equations are solved by a numerical technique taken from the IMSL MATH/LIBRARY. Various results are obtained for the dimensionless temperature profiles in the solid and fluid phases and the radiative heat flux. The effects of some radiative properties of the medium on the heat transfer rate are examined.

The early effects of stavudine compared with tenofovir on adipocyte gene expression, mitochondrial DNA copy number and metabolic parameters in South African HIV-infected patients: a randomized trial.

PubMed

Menezes, C N; Duarte, R; Dickens, C; Dix-Peek, T; Van Amsterdam, D; John, M-A; Ive, P; Maskew, M; Macphail, P; Fox, M P; Raal, F; Sanne, I; Crowther, N J

2013-04-01

Stavudine is being phased out because of its mitochondrial toxicity and tenofovir (TDF) is recommended as part of first-line highly active antiretroviral therapy (HAART) in South Africa. A prospective, open-label, randomized controlled trial comparing standard- and low-dose stavudine with TDF was performed to assess early differences in adipocyte mtDNA copy number, gene expression and metabolic parameters in Black South African HIV-infected patients. Sixty patients were randomized 1:1:1 to either standard-dose (30-40 mg) or low-dose (20-30 mg) stavudine or TDF (300 mg) each combined with lamivudine and efavirenz. Subcutaneous fat biopsies were obtained at weeks 0 and 4. Adipocyte mtDNA copies/cell and gene expression were measured using quantitative polymerase chain reaction (qPCR). Markers of inflammation and lipid and glucose metabolism were also assessed. A 29% and 32% decrease in the mean mtDNA copies/cell was noted in the standard-dose (P < 0.05) and low-dose stavudine (P < 0.005) arms, respectively, when compared with TDF at 4 weeks. Nuclear respiratory factor-1 (NRF1) and mitochondrial cytochrome B (MTCYB) gene expression levels were affected by stavudine, with a significantly (P < 0.05) greater fall in expression observed with the standard, but not the low dose compared with TDF. No significant differences were observed in markers of inflammation and lipid and glucose metabolism. These results demonstrate early mitochondrial depletion among Black South African patients receiving low and standard doses of stavudine, with preservation of gene expression levels, except for NRF1 and MTCYB, when compared with patients on TDF. © 2012 British HIV Association.

Assessing the leaning, bending, and sinuosity of sapling-size trees

Treesearch

Daniel J. Leduc; Shi-Jean S. Sung; Kristi Wharton

2012-01-01

Many factors result in trees with non-straight stems. An important prerequisite to investigating the causes of stem deformity is an ability to assess stem displacement. An ideal system would be easy to implement, be objective, and result in an index that incorporates the essential characteristics of the stem deformity into a dimensionless number. We tested a number of...

Voice Quality Modelling for Expressive Speech Synthesis

PubMed Central

Socoró, Joan Claudi

2014-01-01

This paper presents the perceptual experiments that were carried out in order to validate the methodology of transforming expressive speech styles using voice quality (VoQ) parameters modelling, along with the well-known prosody (F 0, duration, and energy), from a neutral style into a number of expressive ones. The main goal was to validate the usefulness of VoQ in the enhancement of expressive synthetic speech in terms of speech quality and style identification. A harmonic plus noise model (HNM) was used to modify VoQ and prosodic parameters that were extracted from an expressive speech corpus. Perception test results indicated the improvement of obtained expressive speech styles using VoQ modelling along with prosodic characteristics. PMID:24587738

[Sclerostin expression in periodontal ligaments during movement of orthodontic teeth in rats].

PubMed

Yiwen, Chen; Shang, Gao; Tongtong, Xu; Jiahui, Zhang; Jincheng, Li; Huiyan, Zhang; Jinjin, Lu; Min, Hu; Zhihui, Liu

2016-06-01

This study aims to observe the expression of Sclerostin during movement of orthodontic teeth and determine the effect of this protein on remodeling of periodontal tissues. Twenty-four Wistar rats were chosen. Orthodontic forces were applied between the bilateral incisor and first molar to achieve mesial movement. Rats in each group were executed at different time points (0, 1, 3, 5, 7, 14 d). Morphology of periodontal tissue was observed by hematoxylin-eosin (HE) staining. The number of osteoclasts were observed by tartrate-resistant acid phosphatase (TRAP) staining. Sclerostin expression were observed by immunohistochemical staining. HE staining revealed that the resorption of alveolar bone intensified with prolonged movement. Results of immunohistochemical and TRAP staining revealed that Sclerostin expression and number of osteoclasts were related to duration of movement of orthodontic tooth. After staining for 5 days, the number of osteoclasts and Sclerostin expression reached their peak and then began to decline. The numbers of osteoclasts and the expression level of Sclerostin were higher at the compressive side than those at the tensive side. Sclerostin affected orthodontic tooth movement by inhibiting the Wnt signaling pathway and by indirectly or directly controlling bone morphogenetic protein.

Modulation of ColE1-like Plasmid Replication for Recombinant Gene Expression

PubMed Central

Camps, Manel

2010-01-01

ColE1-like plasmids constitute the most popular vectors for recombinant protein expression. ColE1 plasmid replication is tightly controlled by an antisense RNA mechanism that is highly dynamic, tuning plasmid metabolic burden to the physiological state of the host. Plasmid homeostasis is upset upon induction of recombinant protein expression because of non-physiological levels of expression and because of the frequently biased amino acid composition of recombinant proteins. Disregulation of plasmid replication is the main cause of collapse of plasmid-based expression systems because of a simultaneous increase in the metabolic burden (due to increased average copy number) and in the probability of generation of plasmid-free cells (due to increased copy number variation). Interference between regulatory elements of co-resident plasmids causes comparable effects on plasmid stability (plasmid incompatibility). Modulating plasmid copy number for recombinant gene expression aims at achieving a high gene dosage while preserving the stability of the expression system. Here I present strategies targeting plasmid replication for optimizing recombinant gene expression. Specifically, I review approaches aimed at modulating the antisense regulatory system (as well as their implications for plasmid incompatibility) and innovative strategies involving modulation of host factors, of R-loop formation, and of the timing of recombinant gene expression. PMID:20218961

Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules.

PubMed

Tétart, F; Bouché, J P

1992-03-01

We show that the 53-nucleotide RNA molecule encoded by gene dicF blocks cell division in Escherichia coli by inhibiting the translation of ftsZ mRNA. Such a role for dicF had been predicted on the basis of the complementarity of DicF RNA with the ribosome-binding region of the ftsZ mRNA. An analysis of ftsZ expression at its chromosomal locus, and of an ftsZ-lacZ translational fusion controlled by promoters ftsZ1p and ftsZ2p only, indicates that ftsZ is not autoregulated. Partial inhibition of FtsZ synthesis leads to increased cell size. However, the number of FtsZ molecules per cell can be reduced threefold without affecting the division rate significantly. Our results suggest that septation is not triggered by a fixed number of newly synthesized FtsZ molecules per cell.

Effect of timing of development on total cell number and expression profile of HSP-70.1 and GLUT-1 in buffalo (Bubalus bubalis) oocytes and preimplantation embryos produced in vitro.

PubMed

Rajhans, Rajib; Kumar, G Sai; Dubey, Pawan K; Sharma, G Taru

2010-03-29

The present study was designed to compare the expression profile of two developmentally important genes (HSP-70.1 and GLUT-1) and TCN (total cell number) count in fast (group A) and slow (group B) cleaved buffalo embryos to access their in vitro developmental competence. Buffalo COCs (cumulus oocyte complexes) were collected from local abattoir ovaries and subjected to in vitro maturation in: TCM-199 supplemented with 10% FBS (fetal bovine serum), BSA (3 mg/ml), sodium pyruvate (0.25 mM) and 20 ng/ml EGF (epidermal growth factor) at 38.5 degrees C under 5% CO2. In vitro derived embryos were collected at 4-8, 8-16 cell, morula and blastocyst stages at specific time points for gene expression analysis and total cell count. A semiquantitative RT-PCR (reverse transcriptase-PCR) assay was used to determine the HSP-70.1 and GLUT-1 transcripts. Results showed that developmental competence and TCN count in fast (group A)-cleaving embryos was significantly (P<0.05) higher than in the slow group (group B). The gene transcript of HSP-70.1 and GLUT-1 was expressed in oocytes (immature and mature) and throughout the embryonic developmental stages in the fast group (group A), while in the slow (group B) cleaving embryos, the expression of HSP-70.1 was absent in all the embryonic developmental stages, and expression of GLUT-1 was absent after 8-16 cell stage. In conclusion, TCN count and expression profile of HSP-70.1 and GLUT-1 genes in buffalo embryos are different taking into account the cleavage rate. Quality of such embryos for research purposes, TCN and expression profiling of developmentally important genes should be employed to optimize the in vitro culture system to produce superior quality of embryos.

Lubrication Flows.

ERIC Educational Resources Information Center

Papanastasiou, Tasos C.

1989-01-01

Discusses fluid mechanics for undergraduates including the differential Navier-Stokes equations, dimensional analysis and simplified dimensionless numbers, control volume principles, the Reynolds lubrication equation for confined and free surface flows, capillary pressure, and simplified perturbation techniques. Provides a vertical dip coating…

Method of Matching Performance of Compressor Systems with that of Aircraft Power Sections

NASA Technical Reports Server (NTRS)

Bullock, Robert O.; Keetch, Robert C.; Moses, Jason J.

1945-01-01

A method is developed of easily determining the performance of a compressor system relative to that of the power section for a given altitude. Because compressors, reciprocating engines, and turbines are essentially flow devices, the performance of each of these power-plant components is presented in terms of similar dimensionless ratios. The pressure and temperature changes resulting from restrictions of the charge-air flow and from heat transfer in the ducts connecting the components of the power plant are also expressed by the same dimensionless ratios and the losses are included in the performance of the compressor. The performance of a mechanically driven, single-stage compressor in relation to the performance of a conventional air-cooled engine operating at sea-level conditions is presented as an example of the application of the method.

Reynolds analogy for the Rayleigh problem at various flow modes.

PubMed

Abramov, A A; Butkovskii, A V

2016-07-01

The Reynolds analogy and the extended Reynolds analogy for the Rayleigh problem are considered. For a viscous incompressible fluid we derive the Reynolds analogy as a function of the Prandtl number and the Eckert number. We show that for any positive Eckert number, the Reynolds analogy as a function of the Prandtl number has a maximum. For a monatomic gas in the transitional flow regime, using the direct simulation Monte Carlo method, we investigate the extended Reynolds analogy, i.e., the relation between the shear stress and the energy flux transferred to the boundary surface, at different velocities and temperatures. We find that the extended Reynolds analogy for a rarefied monatomic gas flow with the temperature of the undisturbed gas equal to the surface temperature depends weakly on time and is close to 0.5. We show that at any fixed dimensionless time the extended Reynolds analogy depends on the plate velocity and temperature and undisturbed gas temperature mainly via the Eckert number. For Eckert numbers of the order of unity or less we generalize an extended Reynolds analogy. The generalized Reynolds analogy depends mainly only on dimensionless time for all considered Eckert numbers of the order of unity or less.

Arithmetic operations in optical computations using a modified trinary number system.

PubMed

Datta, A K; Basuray, A; Mukhopadhyay, S

1989-05-01

A modified trinary number (MTN) system is proposed in which any binary number can be expressed with the help of trinary digits (1, 0, 1 ). Arithmetic operations can be performed in parallel without the need for carry and borrow steps when binary digits are converted to the MTN system. An optical implementation of the proposed scheme that uses spatial light modulators and color-coded light signals is described.

Limited number of immunoglobulin VH regions expressed in the mutant rabbit "Alicia".

PubMed

DiPietro, L A; Short, J A; Zhai, S K; Kelus, A S; Meier, D; Knight, K L

1990-06-01

A unique feature of rabbit Ig is the presence of VH region allotypic specificities. In normal rabbits, more than 80% of circulating immunoglobulin molecules bear the VHa allotypic specificities, al, a2 or a3; the remaining 10% to 20% of immunoglobulin molecules lack VHa allotypic specificities and are designated VHa-. A mutant rabbit designated Alicia, in contrast, has predominantly serum immunoglobulin molecules that lack the VHa allotypic specificities (Kelus and Weiss, Proc. Natl. Acad. Sci. USA 1986. 83: 4883). To study the nature and molecular complexity of VHa- molecules, we cloned and determined the nucleotide sequence of seven cDNA prepared from splenic RNA of an Alicia rabbit. Six of the clones appeared to encode VHa- molecules; the framework regions encoded by these clones were remarkably similar to each other, each having an unusual insertion of four amino acids at position 10. This insertion of four amino acids has been seen in only 2 of 54 sequenced rabbit VH genes. The similarity of the sequences of the six VHa- clones to each other and their dissimilarity to most other VH genes leads us to suggest that the VHa- molecules in Alicia rabbits are derived predominantly from one or a small number of very similar VH genes. Such preferential utilization of a small number of VH genes may explain the allelic inheritance of VH allotypes.

Cloning, Expression, and Purification of Brucella suis Outer Membrane Proteins

DTIC Science & Technology

2005-01-01

13-09-20061 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Cloning, expression and purification of Brucella suis outer membrane proteins 5b. GRANT NUMBER...attractive for this purpose. In this study, we cloned, expressed and purified seven predicted OMPs of Brucella suis . The recombinant proteins were...fused with 6-his and V5 epitope tags at their C termini to facilitate detection and purification. The B. suis surface genes were PCR synthesized based

Application of dimensionless sediment rating curves to predict suspended-sediment concentrations, bedload, and annual sediment loads for rivers in Minnesota

USGS Publications Warehouse

Ellison, Christopher A.; Groten, Joel T.; Lorenz, David L.; Koller, Karl S.

2016-10-27

Consistent and reliable sediment data are needed by Federal, State, and local government agencies responsible for monitoring water quality, planning river restoration, quantifying sediment budgets, and evaluating the effectiveness of sediment reduction strategies. Heightened concerns about excessive sediment in rivers and the challenge to reduce costs and eliminate data gaps has guided Federal and State interests in pursuing alternative methods for measuring suspended and bedload sediment. Simple and dependable data collection and estimation techniques are needed to generate hydraulic and water-quality information for areas where data are unavailable or difficult to collect.The U.S. Geological Survey, in cooperation with the Minnesota Pollution Control Agency and the Minnesota Department of Natural Resources, completed a study to evaluate the use of dimensionless sediment rating curves (DSRCs) to accurately predict suspended-sediment concentrations (SSCs), bedload, and annual sediment loads for selected rivers and streams in Minnesota based on data collected during 2007 through 2013. This study included the application of DSRC models developed for a small group of streams located in the San Juan River Basin near Pagosa Springs in southwestern Colorado to rivers in Minnesota. Regionally based DSRC models for Minnesota also were developed and compared to DSRC models from Pagosa Springs, Colorado, to evaluate which model provided more accurate predictions of SSCs and bedload in Minnesota.Multiple measures of goodness-of-fit were developed to assess the effectiveness of DSRC models in predicting SSC and bedload for rivers in Minnesota. More than 600 dimensionless ratio values of SSC, bedload, and streamflow were evaluated and delineated according to Pfankuch stream stability categories of “good/fair” and “poor” to develop four Minnesota-based DSRC models. The basis for Pagosa Springs and Minnesota DSRC model effectiveness was founded on measures of goodness

Modeling the number of car theft using Poisson regression

NASA Astrophysics Data System (ADS)

Zulkifli, Malina; Ling, Agnes Beh Yen; Kasim, Maznah Mat; Ismail, Noriszura

2016-10-01

Regression analysis is the most popular statistical methods used to express the relationship between the variables of response with the covariates. The aim of this paper is to evaluate the factors that influence the number of car theft using Poisson regression model. This paper will focus on the number of car thefts that occurred in districts in Peninsular Malaysia. There are two groups of factor that have been considered, namely district descriptive factors and socio and demographic factors. The result of the study showed that Bumiputera composition, Chinese composition, Other ethnic composition, foreign migration, number of residence with the age between 25 to 64, number of employed person and number of unemployed person are the most influence factors that affect the car theft cases. These information are very useful for the law enforcement department, insurance company and car owners in order to reduce and limiting the car theft cases in Peninsular Malaysia.

THE PROCESS OF MASS TRANSFER ON THE SOLID-LIQUID BOUNDARY LAYER DURING THE RELEASE OF DICLOFENAC SODIUM AND PAPAVERINE HYDROCHLORIDE FROM TABLETS IN A PADDLE APPARATUS.

PubMed

Kasperek, Regina; Zimmer, Lukasz; Poleszak, Ewa

2016-01-01

The release study of diclofenac sodium (DIC) and papaverine hydrochloride (PAP) from two formulations of the tablets in the paddle apparatus using different rotation speeds to characterize the process of mass transfer on the solid-liquid boundary layer was carried out. The dissolution process of active substances was described by values of mass transfer coefficients, the diffusion boundary layer thickness and dimensionless numbers (Sh and Re). The values of calculated parameters showed that the release of DIC and PAP from tablets comprising potato starch proceeded faster than from tablets containing HPMC and microcrystalline cellulose. They were obtained by direct dependencies between Sh and Re in the range from 75 rpm to 125 rpm for both substances from all tablets. The description of the dissolution process with the dimensionless numbers make it possible to plan the drug with the required release profile under given in vitro conditions.

Alternative-splicing-mediated gene expression

NASA Astrophysics Data System (ADS)

Wang, Qianliang; Zhou, Tianshou

2014-01-01

Alternative splicing (AS) is a fundamental process during gene expression and has been found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels both quantitatively and qualitatively remains to be fully explored. Here, we analyze two common models of gene expression, each incorporating a simple splice mechanism that a pre-mRNA is spliced into two mature mRNA isoforms in a probabilistic manner. In the constitutive expression case, we show that the steady-state molecular numbers of two mature mRNA isoforms follow mutually independent Poisson distributions. In the bursting expression case, we demonstrate that the tail decay of the steady-state distribution for both mature mRNA isoforms that in general are not mutually independent can be characterized by the product of mean burst size and splicing probability. In both cases, we find that AS can efficiently modulate both the variability (measured by variance) and the noise level of the total mature mRNA, and in particular, the latter is always lower than the noise level of the pre-mRNA, implying that AS always reduces the noise. These results altogether reveal that AS is a mechanism of efficiently controlling the gene expression noise.

The Mhc class II of the Black grouse (Tetrao tetrix) consists of low numbers of B and Y genes with variable diversity and expression.

PubMed

Strand, Tanja; Westerdahl, Helena; Höglund, Jacob; V Alatalo, Rauno; Siitari, Heli

2007-09-01

We found that the Black grouse (Tetrao tetrix) possess low numbers of Mhc class II B (BLB) and Y (YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken (Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc-E gene cluster.

Focal shift and the axial optical coordinate for high-aperture systems of finite Fresnel number.

PubMed

Sheppard, Colin J R; Török, Peter

2003-11-01

Analytic expressions are given for the on-axis intensity predicted by the Rayleigh-Sommerfeld and Kirchhoff diffraction integrals for a scalar optical system of high numerical aperture and finite value of Fresnel number. A definition of the axial optical coordinate is introduced that is valid for finite values of Fresnel number, for high-aperture systems, and for observation points distant from the focus. The focal shift effect is reexamined. For the case when the focal shift is small, explicit expressions are given for the focal shift and the axial peak in intensity.

Identification and resolution of artifacts in the interpretation of imprinted gene expression

PubMed Central

Proudhon, Charlotte

2010-01-01

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression. PMID:20829207

Identification and resolution of artifacts in the interpretation of imprinted gene expression.

PubMed

Proudhon, Charlotte; Bourc'his, Déborah

2010-12-01

Genomic imprinting refers to genes that are epigenetically programmed in the germline to express exclusively or preferentially one allele in a parent-of-origin manner. Expression-based genome-wide screening for the identification of imprinted genes has failed to uncover a significant number of new imprinted genes, probably because of the high tissue- and developmental-stage specificity of imprinted gene expression. A very large number of technical and biological artifacts can also lead to the erroneous evidence of imprinted gene expression. In this article, we focus on three common sources of potential confounding effects: (i) random monoallelic expression in monoclonal cell populations, (ii) genetically determined monoallelic expression and (iii) contamination or infiltration of embryonic tissues with maternal material. This last situation specifically applies to genes that occur as maternally expressed in the placenta. Beside the use of reciprocal crosses that are instrumental to confirm the parental specificity of expression, we provide additional methods for the detection and elimination of these situations that can be misinterpreted as cases of imprinted expression.

Investigation of Processes Controlling Elution of Solutes from Nonaqueous Phase Liquid (NAPL) Pools into Groundwater

NASA Astrophysics Data System (ADS)

Seyedabbasi, M.; Pirestani, K.; Holland, S. B.; Imhoff, P. T.

2005-12-01

Two major processes influencing the elution of solutes from porous media contaminated with nonaqueous phase liquids (NAPLs) are external mass transfer between the NAPL and groundwater and internal diffusion through NAPL ganglia and pools. There is a relatively large body of literature on the dissolution of single-species NAPLs. Less is known about the rates of elution of compounds dissolving from multicomponent NAPLs. We examined the mass transfer of one solute, 2,3-dimethyl-2-butanol (DMB) - a partitioning tracer, between groundwater and a dense NAPL - trichloroethylene (TCE). Diffusion cell experiments were used to measure the molecular diffusion coefficient of DMB in pure TCE and in porous media contaminated with a TCE pool. Measured diffusion coefficients were compared with empirical correlations (pure TCE) and a parallel resistance model (TCE pool). Based on the results from these analyses, a dimensionless Biot number was derived to express the ratio of the external rate of mass transfer from a NAPL pool to the internal rate of diffusion within the pool, which varies with NAPL saturation and NAPL-water partition coefficient. Biot numbers were then estimated for several laboratory scale experiments involving DMB transport between NAPL pools and groundwater. The estimated Biot numbers were in good agreement with experimental results. The expression for the Biot number developed here may be used to assess the processes controlling the elution of solutes from NAPL pools, which has implications on long-term predictions of solute dissolution from NAPLs in the field.

Combined electroosmotically and pressure driven flow in soft nanofluidics.

PubMed

Matin, Meisam Habibi; Ohshima, Hiroyuki

2015-12-15

The present study is devoted to the analysis of mixed electroosmotic and pressure driven flows through a soft charged nanochannel considering boundary slip and constant charge density on the walls of the slit channel. The sources of the fluid flow are the pressure gradient along the channel axis and the electrokinetic effects that trigger an electroosmotic flow under the influence of a uniformly applied electric field. The polyelectrolyte layer (PEL) is denoted as a fixed charge layer (FCL) and the electrolyte ions can be present both inside and outside the PEL i.e., the PEL-electrolyte interface acts as a semi-penetrable membrane. The Poisson-Boltzmann equation is solved assuming the Debye-Hückel linearization for the low electric potential to provide us with analytical closed form solutions for the conservation equations. The conservation equations are solved to obtain the electric potential and velocity distributions in terms of governing dimensionless parameters. The results for the dimensionless electric potential, the dimensionless velocity and Poiseuille number are presented graphically and discussed in detail. Copyright © 2015 Elsevier Inc. All rights reserved.

Nonlinear Dynamics in Viscoelastic Jets

NASA Astrophysics Data System (ADS)

Majmudar, Trushant; Varagnat, Matthieu; McKinley, Gareth

2008-11-01

Instabilities in free surface continuous jets of non-Newtonian fluids, although relevant for many industrial processes, remain poorly understood in terms of fundamental fluid dynamics. Inviscid, and viscous Newtonian jets have been studied in considerable detail, both theoretically and experimentally. Instability in viscous jets leads to regular periodic coiling of the jet, which exhibits a non-trivial frequency dependence with the height of the fall. Here we present a systematic study of the effect of viscoelasticity on the dynamics of continuous jets of worm-like micellar surfactant solutions of varying viscosities and elasticities. We observe complex nonlinear spatio-temporal dynamics of the jet, and uncover a transition from periodic to quasi-periodic to a multi-frequency, broad-spectrum dynamics. Beyond this regime, the jet dynamics smoothly crosses over to exhibit the ``leaping shampoo'' or the Kaye effect. We examine different dynamical regimes in terms of scaling variables, which depend on the geometry (dimensionless height), kinematics (dimensionless flow rate), and the fluid properties (elasto-gravity number) and present a regime map of the dynamics of the jet in terms of these dimensionless variables.

Nonlinear Dynamics in Viscoelastic Jets

NASA Astrophysics Data System (ADS)

Majmudar, Trushant; Varagnat, Matthieu; McKinley, Gareth

2009-03-01

Instabilities in free surface continuous jets of non-Newtonian fluids, although relevant for many industrial processes, remain poorly understood in terms of fundamental fluid dynamics. Inviscid, and viscous Newtonian jets have been studied in considerable detail, both theoretically and experimentally. Instability in viscous jets leads to regular periodic coiling of the jet, which exhibits a non-trivial frequency dependence with the height of the fall. Here we present a systematic study of the effect of viscoelasticity on the dynamics of continuous jets of worm-like micellar surfactant solutions of varying viscosities and elasticities. We observe complex nonlinear spatio-temporal dynamics of the jet, and uncover a transition from periodic to quasi-periodic to a multi-frequency, broad-spectrum dynamics. Beyond this regime, the jet dynamics smoothly crosses over to exhibit the ``leaping shampoo'' or the Kaye effect. We examine different dynamical regimes in terms of scaling variables, which depend on the geometry (dimensionless height), kinematics (dimensionless flow rate), and the fluid properties (elasto-gravity number) and present a regime map of the dynamics of the jet in terms of these dimensionless variables.

Self-similar Theory of Wind-driven Sea

NASA Astrophysics Data System (ADS)

Zakharov, V. E.

2015-12-01

More than two dozens field experiments performed in the ocean and on the lakes show that the fetch-limited growth of dimensionless energy and dimensionless peak frequency is described by powerlike functions of the dimensionless fetch. Moreover, the exponents of these two functions are connected with a proper accuracy by the standard "magic relation", 10q-2p=1. Recent massive numerical experiments as far as experiments in wave tanks also confirm this magic relation. All these experimental facts can be interpreted in a framework of the following simple theory. The wind-driven sea is described by the "conservative" Hasselmann kinetic equation. The source terms, wind input and white-capping dissipation, play a secondary role in comparison with the nonlinear term Snl that is responsible for the four-wave resonant interaction. This equation has four-parameter family of self-similar solutions. The magic relation holds for all numbers of this family. This fact gives strong hope that development of self-consistent analytic theory of wind-driven sea is quite realizable task.

Dual transcriptional-translational cascade permits cellular level tuneable expression control

PubMed Central

Morra, Rosa; Shankar, Jayendra; Robinson, Christopher J.; Halliwell, Samantha; Butler, Lisa; Upton, Mathew; Hay, Sam; Micklefield, Jason; Dixon, Neil

2016-01-01

The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The discovery, design and reengineering of riboswitches offer an alternative means by which to control gene expression. Here we report the development and characterization of a novel tunable recombinant expression system, termed RiboTite, which operates at both the transcriptional and translational level. Using standard inducible promoters and orthogonal riboswitches, a multi-layered modular genetic control circuit was developed to control the expression of both bacteriophage T7 RNA polymerase and recombinant gene(s) of interest. The system was benchmarked against a number of commonly used E. coli expression systems, and shows tight basal control, precise analogue tunability of gene expression at the cellular level, dose-dependent regulation of protein production rates over extended growth periods and enhanced cell viability. This novel system expands the number of E. coli expression systems for use in recombinant protein production and represents a major performance enhancement over and above the most widely used expression systems. PMID:26405200

An Analysis of microRNA Expression in the Myelodysplastic Syndromes Using Hematopoietic Stem Cells

DTIC Science & Technology

2014-08-01

AWARD NUMBER: W81XWH-13-1-0082 TITLE: An Analysis of microRNA Expression in the Myelodysplastic Syndromes Using Hematopoietic Stem Cells ... Hematopoietic Stem Cells 5b. GRANT NUMBER W81XWH-13-1-0082 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Dr. Stephen Chung 5e. TASK...in MDS hematopoietic stem cells (MDS HSCs) as compared with normal HSCs. MiRNAs differentially expressed between MDS HSCs and normal HSCs overlapped

Some properties of the Catalan-Qi function related to the Catalan numbers.

PubMed

Qi, Feng; Mahmoud, Mansour; Shi, Xiao-Ting; Liu, Fang-Fang

2016-01-01

In the paper, the authors find some properties of the Catalan numbers, the Catalan function, and the Catalan-Qi function which is a generalization of the Catalan numbers. Concretely speaking, the authors present a new expression, asymptotic expansions, integral representations, logarithmic convexity, complete monotonicity, minimality, logarithmically complete monotonicity, a generating function, and inequalities of the Catalan numbers, the Catalan function, and the Catalan-Qi function. As by-products, an exponential expansion and a double inequality for the ratio of two gamma functions are derived.

Electron number probability distributions for correlated wave functions.

PubMed

Francisco, E; Martín Pendás, A; Blanco, M A

2007-03-07

Efficient formulas for computing the probability of finding exactly an integer number of electrons in an arbitrarily chosen volume are only known for single-determinant wave functions [E. Cances et al., Theor. Chem. Acc. 111, 373 (2004)]. In this article, an algebraic method is presented that extends these formulas to the case of multideterminant wave functions and any number of disjoint volumes. The derived expressions are applied to compute the probabilities within the atomic domains derived from the space partitioning based on the quantum theory of atoms in molecules. Results for a series of test molecules are presented, paying particular attention to the effects of electron correlation and of some numerical approximations on the computed probabilities.

Electrochemical Engineering.

ERIC Educational Resources Information Center

Alkire, Richard C.

1983-01-01

Discusses engineering ramifications of electrochemistry, focusing on current/potential distribution, evaluation of trade-offs between influences of different phenomena, use of dimensionless numbers to assist in scale-over to new operating conditions, and economics. Also provides examples of electrochemical engineering education content related to…

Transformation and model choice for RNA-seq co-expression analysis.

PubMed

Rau, Andrea; Maugis-Rabusseau, Cathy

2018-05-01

Although a large number of clustering algorithms have been proposed to identify groups of co-expressed genes from microarray data, the question of if and how such methods may be applied to RNA sequencing (RNA-seq) data remains unaddressed. In this work, we investigate the use of data transformations in conjunction with Gaussian mixture models for RNA-seq co-expression analyses, as well as a penalized model selection criterion to select both an appropriate transformation and number of clusters present in the data. This approach has the advantage of accounting for per-cluster correlation structures among samples, which can be strong in RNA-seq data. In addition, it provides a rigorous statistical framework for parameter estimation, an objective assessment of data transformations and number of clusters and the possibility of performing diagnostic checks on the quality and homogeneity of the identified clusters. We analyze four varied RNA-seq data sets to illustrate the use of transformations and model selection in conjunction with Gaussian mixture models. Finally, we propose a Bioconductor package coseq (co-expression of RNA-seq data) to facilitate implementation and visualization of the recommended RNA-seq co-expression analyses.

Enhanced expression of VEGF-A in β cells increases endothelial cell number but impairs islet morphogenesis and β cell proliferation

PubMed Central

Cai, Qing; Brissova, Marcela; Reinert, Rachel B.; Pan, Fong Cheng; Brahmachary, Priyanka; Jeansson, Marie; Shostak, Alena; Radhika, Aramandla; Poffenberger, Greg; Quaggin, Susan E.; Jerome, W. Gray; Dumont, Daniel J.; Powers, Alvin C.

2012-01-01

There is a reciprocal interaction between pancreatic islet cells and vascular endothelial cells (EC) in which EC-derived signals promote islet cell differentiation and islet development while islet cell-derived angiogenic factors promote EC recruitment and extensive islet vascularization. To examine the role of angiogenic factors in the coordinated development of islets and their associated vessels, we used a “tet-on” inducible system (mice expressing rat insulin promoter-reverse tetracycline activator transgene and a tet-operon-angiogenic factor transgene) to increase the β cell production of vascular endothelial growth factor-A (VEGF-A), angiopoietin-1 (Ang1), or angiopoietin-2 (Ang2) during islet cell differentiation and islet development. In VEGF-A overexpressing embryos, ECs began to accumulate around epithelial tubes residing in the central region of the developing pancreas (associated with endocrine cells) as early as embryonic day 12.5 (E12.5) and increased dramatically by E16.5. While α and β cells formed islet cell clusters in control embryos at E16.5, the increased EC population perturbed endocrine cell differentiation and islet cell clustering in VEGF-A overexpressing embryos. With continued overexpression of VEGF-A, α and β cells became scattered, remained adjacent to ductal structures, and never coalesced into islets, resulting in a reduction in β cell proliferation and β cell mass at postnatal day 1. A similar impact on islet morphology was observed when VEGF-A was overexpressed in β cells during the postnatal period. In contrast, increased expression of Ang1 or Ang2 in β cells in developing or adult islets did not alter islet differentiation, development, or morphology, but altered islet EC ultrastructure. These data indicate that 1) increased EC number does not promote, but actually impairs β cell proliferation and islet formation; 2) the level of VEGF-A production by islet endocrine cells is critical for islet vascularization during

An effective fuzzy kernel clustering analysis approach for gene expression data.

PubMed

Sun, Lin; Xu, Jiucheng; Yin, Jiaojiao

2015-01-01

Fuzzy clustering is an important tool for analyzing microarray data. A major problem in applying fuzzy clustering method to microarray gene expression data is the choice of parameters with cluster number and centers. This paper proposes a new approach to fuzzy kernel clustering analysis (FKCA) that identifies desired cluster number and obtains more steady results for gene expression data. First of all, to optimize characteristic differences and estimate optimal cluster number, Gaussian kernel function is introduced to improve spectrum analysis method (SAM). By combining subtractive clustering with max-min distance mean, maximum distance method (MDM) is proposed to determine cluster centers. Then, the corresponding steps of improved SAM (ISAM) and MDM are given respectively, whose superiority and stability are illustrated through performing experimental comparisons on gene expression data. Finally, by introducing ISAM and MDM into FKCA, an effective improved FKCA algorithm is proposed. Experimental results from public gene expression data and UCI database show that the proposed algorithms are feasible for cluster analysis, and the clustering accuracy is higher than the other related clustering algorithms.

Neurochemical phenotype of cytoglobin-expressing neurons in the rat hippocampus.

PubMed

Hundahl, Christian Ansgar; Fahrenkrug, Jan; Hannibal, Jens

2014-09-01

Cytoglobin (Cygb), a novel oxygen-binding protein, is expressed in the majority of tissues and has been proposed to function in nitric oxide (NO) metabolism in the vasculature and to have cytoprotective properties. However, the overall functions of Cygb remain elusive. Cygb is also expressed in a subpopulation of brain neurons. Recently, it has been shown that stress upregulates Cygb expression in the brain and the majority of neuronal nitric oxide synthase (nNOS)-positive neurons, an enzyme that produces NO, co-express Cygb. However, there are more neurons expressing Cygb than nNOS, thus a large number of Cygb neurons remain uncharacterized by the neurochemical content. The aim of the present study was to provide an additional and more detailed neurochemical phenotype of Cygb-expressing neurons in the rat hippocampus. The rat hippocampus was chosen due to the abundance of Cygb, as well as this limbic structure being an important target in a number of neurodegenerative diseases. Using triple immunohistochemistry, it was demonstrated that nearly all the parvalbumin- and heme oxygenase 1-positive neurons co-express Cygb and to a large extent, these neuron populations are distinct from the population of Cygb neurons co-expressing nNOS. Furthermore, it was shown that the majority of neurons expressing somastostatin and vasoactive intestinal peptide also co-express Cygb and nNOS. Detailed information regarding the neurochemical phenotype of Cygb neurons in the hippocampus can be a valuable tool in determining the function of Cygb in the brain.

A cell-ELISA for the quantification of adherent murine macrophages and the surface expression of antigens.

PubMed

Nibbering, P H; Van de Gevel, J S; Van Furth, R

1990-07-20

The present study was performed in order to establish whether a cell-ELISA could be used to determine the expression of antigens by adherent murine peritoneal macrophages and also quantify the numbers of such macrophages. Accurate determination of the number of adherent macrophages proved to be possible with a cell-ELISA designed to assess complement receptor type III (CRIII) expression. Expression of CRIII was considerably more sensitive than determination of the cell-protein or DNA content as a measure of the number of adherent macrophages. For the calculation of the expression of CRIII, Ia antigen, and antigen F4/80 by resident and activated macrophages, use was made of the linear part of the curve obtained when the numbers of macrophages were plotted against the absorbance values for each of the antigens. The values for CRIII expression did not differ significantly between resident macrophages, macrophages activated with recombinant interferon-gamma (rIFN-gamma) and macrophages activated with BCG/PPD. IFN-gamma-activated and BCG/PPD-activated macrophages expressed Ia antigen significantly more intensely than did resident peritoneal macrophages. In contrast the activated macrophages expressed F4/80 significantly less intensely than resident peritoneal macrophages.

Design Model for the Heat Transfer in a Short Straight Tube Boiler.

DTIC Science & Technology

1981-06-01

Equilibrium Quality XT - True Quality XTT - Martinelli Parameter Dimensionless Groups Nu - Nusselt Number Pr - Prandtl Number Re - Reynolds Number...fill a cylinder in which a piston was mounted. When the steam was suddenly condensed by a spray of water, a partial vacuum was created, and the piston...BOILER - 1725 SFET YAL OOS _ FIGURE 6: JAMES WATTS WAGON-TYPE BOILER - 1785 25 water-inlet, a condensate return, a steam outlet, a gauge glass for

Hazardous waste incinerators under waste uncertainty: balancing and throughput maximization via heat recuperation.

PubMed

Tsiliyannis, Christos Aristeides

2013-09-01

Hazardous waste incinerators (HWIs) differ substantially from thermal power facilities, since instead of maximizing energy production with the minimum amount of fuel, they aim at maximizing throughput. Variations in quantity or composition of received waste loads may significantly diminish HWI throughput (the decisive profit factor), from its nominal design value. A novel formulation of combustion balance is presented, based on linear operators, which isolates the wastefeed vector from the invariant combustion stoichiometry kernel. Explicit expressions for the throughput are obtained, in terms of incinerator temperature, fluegas heat recuperation ratio and design parameters, for an arbitrary number of wastes, based on fundamental principles (mass and enthalpy balances). The impact of waste variations, of recuperation ratio and of furnace temperature is explicitly determined. It is shown that in the presence of waste uncertainty, the throughput may be a decreasing or increasing function of incinerator temperature and recuperation ratio, depending on the sign of a dimensionless parameter related only to the uncertain wastes. The dimensionless parameter is proposed as a sharp a' priori waste 'fingerprint', determining the necessary increase or decrease of manipulated variables (recuperation ratio, excess air, auxiliary fuel feed rate, auxiliary air flow) in order to balance the HWI and maximize throughput under uncertainty in received wastes. A 10-step procedure is proposed for direct application subject to process capacity constraints. The results may be useful for efficient HWI operation and for preparing hazardous waste blends. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quadratic Expressions by Means of "Summing All the Matchsticks"

ERIC Educational Resources Information Center

Gierdien, M. Faaiz

2012-01-01

This note presents demonstrations of quadratic expressions that come about when particular problems are posed with respect to matchsticks that form regular triangles, squares, pentagons and so on. Usually when such "matchstick" problems are used as ways to foster algebraic thinking, the expressions for the number of matchstick quantities are…

BeadArray Expression Analysis Using Bioconductor

PubMed Central

Ritchie, Matthew E.; Dunning, Mark J.; Smith, Mike L.; Shi, Wei; Lynch, Andy G.

2011-01-01

Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies. Aside from the vendor-provided software tools for analyzing BeadArray expression data (GenomeStudio/BeadStudio), there exists a comprehensive set of open-source analysis tools in the Bioconductor project, many of which have been tailored to exploit the unique properties of this platform. In this article, we explore a number of these software packages and demonstrate how to perform a complete analysis of BeadArray data in various formats. The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered. PMID:22144879

New Bedform Phase Diagrams and Discriminant Functions for Formative Conditions of Bedforms in Open-Channel Flows

NASA Astrophysics Data System (ADS)

Ohata, Koji; Naruse, Hajime; Yokokawa, Miwa; Viparelli, Enrica

2017-11-01

Understanding of the formative conditions of fluvial bedforms is significant for both river management and geological studies. Diagrams showing bedform stability conditions have been widely used for the analyses of sedimentary structures. However, the use of discriminants to determine the boundaries of different bedforms regimes has not yet been explored. In this study, we use discriminant functions to describe formative conditions for a range of fluvial bedforms in a 3-D dimensionless parametric space. We do this by means of discriminant analysis using the Mahalanobis distance. We analyzed 3,793 available laboratory and field data and used these to produce new bedform phase diagrams. These diagrams employ three dimensionless parameters representing properties of flow hydraulics and sediment particles as their axes. The discriminant functions for bedform regimes proposed herein are quadratic functions of three dimensionless parameters and are expressed as curved surfaces in 3-D space. These empirical functions can be used to estimate paleoflow velocities from sedimentary structures. As an example of the reconstruction of hydraulic conditions, we calculated the paleoflow velocity of the 2011 Tohoku-Oki tsunami backwash flow from the sedimentary structures of the tsunami deposit. In so doing, we successfully reconstructed reasonable values of the paleoflow velocities.

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

PubMed Central

Maron, Lyza G.; Guimarães, Claudia T.; Kirst, Matias; Albert, Patrice S.; Birchler, James A.; Bradbury, Peter J.; Buckler, Edward S.; Coluccio, Alison E.; Danilova, Tatiana V.; Kudrna, David; Magalhaes, Jurandir V.; Piñeros, Miguel A.; Schatz, Michael C.; Wing, Rod A.; Kochian, Leon V.

2013-01-01

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world’s potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments. PMID:23479633

Number Sense on the Number Line

ERIC Educational Resources Information Center

Woods, Dawn Marie; Ketterlin Geller, Leanne; Basaraba, Deni

2018-01-01

A strong foundation in early number concepts is critical for students' future success in mathematics. Research suggests that visual representations, like a number line, support students' development of number sense by helping them create a mental representation of the order and magnitude of numbers. In addition, explicitly sequencing instruction…

From rational numbers to algebra: separable contributions of decimal magnitude and relational understanding of fractions.

PubMed

DeWolf, Melissa; Bassok, Miriam; Holyoak, Keith J

2015-05-01

To understand the development of mathematical cognition and to improve instructional practices, it is critical to identify early predictors of difficulty in learning complex mathematical topics such as algebra. Recent work has shown that performance with fractions on a number line estimation task predicts algebra performance, whereas performance with whole numbers on similar estimation tasks does not. We sought to distinguish more specific precursors to algebra by measuring multiple aspects of knowledge about rational numbers. Because fractions are the first numbers that are relational expressions to which students are exposed, we investigated how understanding the relational bipartite format (a/b) of fractions might connect to later algebra performance. We presented middle school students with a battery of tests designed to measure relational understanding of fractions, procedural knowledge of fractions, and placement of fractions, decimals, and whole numbers onto number lines as well as algebra performance. Multiple regression analyses revealed that the best predictors of algebra performance were measures of relational fraction knowledge and ability to place decimals (not fractions or whole numbers) onto number lines. These findings suggest that at least two specific components of knowledge about rational numbers--relational understanding (best captured by fractions) and grasp of unidimensional magnitude (best captured by decimals)--can be linked to early success with algebraic expressions. Copyright © 2015 Elsevier Inc. All rights reserved.

Stochastic field-line wandering in magnetic turbulence with shear. II. Decorrelation trajectory method

NASA Astrophysics Data System (ADS)

Negrea, M.; Petrisor, I.; Shalchi, A.

2017-11-01

We study the diffusion of magnetic field lines in turbulence with magnetic shear. In the first part of the series, we developed a quasi-linear theory for this type of scenario. In this article, we employ the so-called DeCorrelation Trajectory method in order to compute the diffusion coefficients of stochastic magnetic field lines. The magnetic field configuration used here contains fluctuating terms which are described by the dimensionless functions bi(X, Y, Z), i = (x, y) and they are assumed to be Gaussian processes and are perpendicular with respect to the main magnetic field B0. Furthermore, there is also a z-component of the magnetic field depending on radial coordinate x (representing the gradient of the magnetic field) and a poloidal average component. We calculate the diffusion coefficients for magnetic field lines for different values of the magnetic Kubo number K, the dimensionless inhomogeneous magnetic parallel and perpendicular Kubo numbers KB∥, KB⊥ , as well as Ka v=bya vKB∥/KB⊥ .

Evolutionary design of a generalized polynomial neural network for modelling sediment transport in clean pipes

NASA Astrophysics Data System (ADS)

Ebtehaj, Isa; Bonakdari, Hossein; Khoshbin, Fatemeh

2016-10-01

To determine the minimum velocity required to prevent sedimentation, six different models were proposed to estimate the densimetric Froude number (Fr). The dimensionless parameters of the models were applied along with a combination of the group method of data handling (GMDH) and the multi-target genetic algorithm. Therefore, an evolutionary design of the generalized GMDH was developed using a genetic algorithm with a specific coding scheme so as not to restrict connectivity configurations to abutting layers only. In addition, a new preserving mechanism by the multi-target genetic algorithm was utilized for the Pareto optimization of GMDH. The results indicated that the most accurate model was the one that used the volumetric concentration of sediment (CV), relative hydraulic radius (d/R), dimensionless particle number (Dgr) and overall sediment friction factor (λs) in estimating Fr. Furthermore, the comparison between the proposed method and traditional equations indicated that GMDH is more accurate than existing equations.

Multiscale deformation of a liquid surface in interaction with a nanoprobe

NASA Astrophysics Data System (ADS)

Ledesma-Alonso, R.; Tordjeman, P.; Legendre, D.

2012-06-01

The interaction between a nanoprobe and a liquid surface is studied. The surface deformation depends on physical and geometric parameters, which are depicted by employing three dimensionless parameters: Bond number Bo, modified Hamaker number Ha, and dimensionless separation distance D*. The evolution of the deformation is described by a strongly nonlinear partial differential equation, which is solved by means of numerical methods. The dynamic analysis of the liquid profile points out the existence of a critical distance Dmin*, below which the irreversible wetting process of the nanoprobe happens. For D*≥Dmin*, the numerical results show the existence of two deformation profiles, one stable and another unstable from the energetic point of view. Different deformation length-scales, characterizing the stable liquid equilibrium interface, define the near- and the far-field deformation zones, where self-similar profiles are found. Finally, our results allow us to provide simple relationships between the parameters, which leads to determine the optimal conditions when performing atomic force microscope measurements over liquids.

A comparison of facial expression properties in five hylobatid species.

PubMed

Scheider, Linda; Liebal, Katja; Oña, Leonardo; Burrows, Anne; Waller, Bridget

2014-07-01

Little is known about facial communication of lesser apes (family Hylobatidae) and how their facial expressions (and use of) relate to social organization. We investigated facial expressions (defined as combinations of facial movements) in social interactions of mated pairs in five different hylobatid species belonging to three different genera using a recently developed objective coding system, the Facial Action Coding System for hylobatid species (GibbonFACS). We described three important properties of their facial expressions and compared them between genera. First, we compared the rate of facial expressions, which was defined as the number of facial expressions per units of time. Second, we compared their repertoire size, defined as the number of different types of facial expressions used, independent of their frequency. Third, we compared the diversity of expression, defined as the repertoire weighted by the rate of use for each type of facial expression. We observed a higher rate and diversity of facial expression, but no larger repertoire, in Symphalangus (siamangs) compared to Hylobates and Nomascus species. In line with previous research, these results suggest siamangs differ from other hylobatids in certain aspects of their social behavior. To investigate whether differences in facial expressions are linked to hylobatid socio-ecology, we used a Phylogenetic General Least Square (PGLS) regression analysis to correlate those properties with two social factors: group-size and level of monogamy. No relationship between the properties of facial expressions and these socio-ecological factors was found. One explanation could be that facial expressions in hylobatid species are subject to phylogenetic inertia and do not differ sufficiently between species to reveal correlations with factors such as group size and monogamy level. © 2014 Wiley Periodicals, Inc.

Further summation formulae related to generalized harmonic numbers

NASA Astrophysics Data System (ADS)

Zheng, De-Yin

2007-11-01

By employing the univariate series expansion of classical hypergeometric series formulae, Shen [L.-C. Shen, Remarks on some integrals and series involving the Stirling numbers and [zeta](n), Trans. Amer. Math. Soc. 347 (1995) 1391-1399] and Choi and Srivastava [J. Choi, H.M. Srivastava, Certain classes of infinite series, Monatsh. Math. 127 (1999) 15-25; J. Choi, H.M. Srivastava, Explicit evaluation of Euler and related sums, Ramanujan J. 10 (2005) 51-70] investigated the evaluation of infinite series related to generalized harmonic numbers. More summation formulae have systematically been derived by Chu [W. Chu, Hypergeometric series and the Riemann Zeta function, Acta Arith. 82 (1997) 103-118], who developed fully this approach to the multivariate case. The present paper will explore the hypergeometric series method further and establish numerous summation formulae expressing infinite series related to generalized harmonic numbers in terms of the Riemann Zeta function [zeta](m) with m=5,6,7, including several known ones as examples.

Double emulsion formation through hierarchical flow-focusing microchannel

NASA Astrophysics Data System (ADS)

Azarmanesh, Milad; Farhadi, Mousa; Azizian, Pooya

2016-03-01

A microfluidic device is presented for creating double emulsions, controlling their sizes and also manipulating encapsulation processes. As a result of three immiscible liquids' interaction using dripping instability, double emulsions can be produced elegantly. Effects of dimensionless numbers are investigated which are Weber number of the inner phase (Wein), Capillary number of the inner droplet (Cain), and Capillary number of the outer droplet (Caout). They affect the formation process, inner and outer droplet size, and separation frequency. Direct numerical simulation of governing equations was done using volume of fluid method and adaptive mesh refinement technique. Two kinds of double emulsion formation, the two-step and the one-step, were simulated in which the thickness of the sheath of double emulsions can be adjusted. Altering each dimensionless number will change detachment location, outer droplet size and droplet formation period. Moreover, the decussate regime of the double-emulsion/empty-droplet is observed in low Wein. This phenomenon can be obtained by adjusting the Wein in which the maximum size of the sheath is discovered. Also, the results show that Cain has significant influence on the outer droplet size in the two-step process, while Caout affects the sheath in the one-step formation considerably.

Performance analysis and optimization for generalized quantum Stirling refrigeration cycle with working substance of a particle confined in a general 1D potential

NASA Astrophysics Data System (ADS)

Yin, Yong; Chen, Lingen; Wu, Feng

2018-03-01

A generalized irreversible quantum Stirling refrigeration cycle (GIQSRC) is proposed. The working substance of the GIQSRC is a particle confined in a general 1D potential which energy spectrum can be expressed as εn = ℏωnσ . Heat leakage and non-ideal regeneration loss are taken into account. The expressions of coefficient of performance (COP) and dimensionless cooling load are obtained. The different practical cases of the energy spectrum are analyzed. The results of this paper are meaningful to understand the quantum thermodynamics cycles with a particle confined in different potential as working substance.

Prostate Expression Databases: Gene Expression Resources for Comparative Studies of Prostate Carcinogenesis

DTIC Science & Technology

2008-01-01

lesions of low -grade prostatic intraepithelial neoplasia (PIN). Over time, osteopontin expressing dysplastic cells seemed to increase in number in high...neoplasia (PIN) lesions, not seen at 2.5 months, were mostly low grade at 12 months and then turning to an abundant combination of low -grade PIN...Prostate specific antigen (PSA) allows the diagnosis of low grade, localized PCa, that allows the physician to offer the patient several efficacious

Factors for C-Kit Expression in Cardiac Outgrowth Cells and Human Heart Tissue.

PubMed

Matsushita, Satoshi; Minematsu, Kazuo; Yamamoto, Taira; Inaba, Hirotaka; Kuwaki, Kenji; Shimada, Akie; Yokoyama, Yasutaka; Amano, Atsushi

2017-12-12

We determined the factors associated with the expression of c-kit in the heart and the proliferation of c-kit-positive (c-kit pos ) cardiac stem cells among the outgrowth cells cultured from human cardiac explants.Samples of the right atrium (RA), left atrium (LA), and left ventricle obtained from patients during open-heart surgery were processed for cell culture of outgrowth cells and tissue analysis. The total number of growing cells and the population of c-kit pos cells were measured and compared with c-kit expression in native tissues and characteristics of the patients according to the region of the heart.We analyzed 452 samples from 334 patients. Atrial fibrillation (AF) in the patients reduced the number of outgrowth cells from the RA and LA, and aging was a co-factor for the LA. The c-kit pos population from the RA was associated with serum brain natriuretic peptide (BNP). C-kit expression in native tissue was also associated with BNP expression. However, we observed no relationship in expression between outgrowth cells and native tissue. In addition, the RA tissue provided the highest number of c-kit pos cells, and the left ventricle provided the lowest.C-kit was weakly expressed in response to damage. In addition, no correlation between outgrowth cells and native tissue was found for c-kit expression.

Dynamic Modeling for Development and Education: From Concepts to Numbers

ERIC Educational Resources Information Center

Van Geert, Paul

2014-01-01

The general aim of the article is to teach the reader how to transform conceptual models of change, development, and learning into mathematical expressions and how to use these equations to build dynamic models by means of the widely used spreadsheet program Excel. The explanation is supported by a number of Excel files, which the reader can…

Differential microRNA expression is associated with androgen receptor expression in breast cancer.

PubMed

Shi, Yaqin; Yang, Fang; Sun, Zijia; Zhang, Wenwen; Gu, Jun; Guan, Xiaoxiang

2017-01-01

The androgen receptor (AR) is frequently expressed in breast cancer; however, its prognostic value remains unclear. AR expression in breast cancer has been associated with improved outcomes in estrogen receptor (ER)‑positive breast cancer compared with ER‑negative disease. Eliminating AR function in breast cancer is critically important for breast cancer progression. However, the mechanism underlying AR regulation remains poorly understood. The study of microRNAs (miRNAs) has provided important insights into the pathogenesis of hormone‑dependent cancer. To determine whether miRNAs function in the AR regulation of breast cancer, the present study performed miRNA expression profiling in AR‑positive and ‑negative breast cancer cell lines. A total of 153 miRNAs were differentially expressed in AR‑positive compared with AR‑negative breast cancer cells; 52 were upregulated and 101 were downregulated. A number of these have been extensively associated with breast cancer cell functions, including proliferation, invasion and drug‑resistance. Furthermore, through pathway enrichment analysis, signaling pathways associated with the prediction targets of the miRNAs were characterized, including the vascular endothelial growth factor and mammalian target of rapamycin signaling pathways. In conclusion, the results of the present study indicated that the expression of miRNAs may be involved in the mechanism underlying AR regulation of breast cancer, and may improve understanding of the role of AR in breast cancer.

Differential adipokine receptor expression on circulating leukocyte subsets in lean and obese children.

PubMed

Keustermans, Genoveva; van der Heijden, Laila B; Boer, Berlinda; Scholman, Rianne; Nuboer, Roos; Pasterkamp, Gerard; Prakken, Berent; de Jager, Wilco; Kalkhoven, Eric; Janse, Arieke J; Schipper, Henk S

2017-01-01

Childhood obesity prevalence has increased worldwide and is an important risk factor for type 2 diabetes (T2D) and cardiovascular disease (CVD). The production of inflammatory adipokines by obese adipose tissue contributes to the development of T2D and CVD. While levels of circulating adipokines such as adiponectin and leptin have been established in obese children and adults, the expression of adiponectin and leptin receptors on circulating immune cells can modulate adipokine signalling, but has not been studied so far. Here, we aim to establish the expression of adiponectin and leptin receptors on circulating immune cells in obese children pre and post-lifestyle intervention compared to normal weight control children. 13 obese children before and after a 1-year lifestyle intervention were compared with an age and sex-matched normal weight control group of 15 children. Next to routine clinical and biochemical parameters, circulating adipokines were measured, and flow cytometric analysis of adiponectin receptor 1 and 2 (AdipoR1, AdipoR2) and leptin receptor expression on peripheral blood mononuclear cell subsets was performed. Obese children exhibited typical clinical and biochemical characteristics compared to controls, including a higher BMI-SD, blood pressure and circulating leptin levels, combined with a lower insulin sensitivity index (QUICKI). The 1-year lifestyle intervention resulted in stabilization of their BMI-SD. Overall, circulating leukocyte subsets showed distinct adipokine receptor expression profiles. While monocytes expressed high levels of all adipokine receptors, NK and iNKT cells predominantly expressed AdipoR2, and B-lymphocytes and CD4+ and CD8+ T-lymphocyte subsets expressed AdipoR2 as well as leptin receptor. Strikingly though, leukocyte subset numbers and adipokine receptor expression profiles were largely similar in obese children and controls. Obese children showed higher naïve B-cell numbers, and pre-intervention also higher numbers of

Connected Representations of Knowledge: Do Undergraduate Students Relate Algebraic Rational Expressions to Rational Numbers?

ERIC Educational Resources Information Center

Yantz. Jennifer

2013-01-01

The attainment and retention of later algebra skills in high school has been identified as a factor significantly impacting students' postsecondary success as STEM majors. Researchers maintain that learners develop meaning for algebraic procedures by forming connections to the basic number system properties. In the present study, the connections…

VGF expression by T lymphocytes in patients with Alzheimer's disease

PubMed Central

Glorius, Sarah; Dobrowolny, Henrik; Greiner-Bohl, Sabrina; Mawrin, Christian; Bommhardt, Ursula; Hartig, Roland; Bogerts, Bernhard; Busse, Mandy

2015-01-01

Secretion of VGF is increased in cerebrospinal fluid and blood in neurodegenerative disorders like Alzheimer's disease (AD) and VGF is a potential biomarker for these disorders. We have shown that VGF is expressed in peripheral T cells and is correlated with T cell survival and cytokine secretion. The frequency of VGF+CD3+ T cells increases with normal aging. We found an increased number of VGF-expressing T cells in patients with AD compared to aged healthy controls, which was associated with enhanced HbA1c levels in blood. Upon treatment with rivastigmine, T cell proliferation and VGF expression in AD patients decreased to the level found in controls. Moreover, rapamycin treatment in vitro reduced the number of VGF+CD3+ cells in AD patients to control levels. PMID:26142708

Judgments of subtle facial expressions of emotion.

PubMed

Matsumoto, David; Hwang, Hyisung C

2014-04-01

Most studies on judgments of facial expressions of emotion have primarily utilized prototypical, high-intensity expressions. This paper examines judgments of subtle facial expressions of emotion, including not only low-intensity versions of full-face prototypes but also variants of those prototypes. A dynamic paradigm was used in which observers were shown a neutral expression followed by the target expression to judge, and then the neutral expression again, allowing for a simulation of the emergence of the expression from and then return to a baseline. We also examined how signal and intensity clarities of the expressions (explained more fully in the Introduction) were associated with judgment agreement levels. Low-intensity, full-face prototypical expressions of emotion were judged as the intended emotion at rates significantly greater than chance. A number of the proposed variants were also judged as the intended emotions. Both signal and intensity clarities were individually associated with agreement rates; when their interrelationships were taken into account, signal clarity independently predicted agreement rates but intensity clarity did not. The presence or absence of specific muscles appeared to be more important to agreement rates than their intensity levels, with the exception of the intensity of zygomatic major, which was positively correlated with agreement rates for judgments of joy.

Influence of neighboring particles on the drag of a particle suspended in laminar flows

NASA Astrophysics Data System (ADS)

Roig, Adam Vincent

Understanding particle-fluid flows is very important for the areas of sedimentation in river beds, fluidized bed reactors, and other fields of multiphase flow. The effect of one particle on another in a fluid flow is not very well understood nor does a correlation exist to describe the behavior of the drag coefficient between particles. The use of Proteus was validated by comparison to previous studies to the result obtained through simulations in Proteus, including analysis of the wake structure of a single sphere. Two particles were then analyzed for various Reynolds numbers less than 250 but greater than 5 and for the dimensionless gap of L/D ≥ 2, where L is the distance between the two particle centers and D is the diameter of the particles. Two arrangements were used for simulation, with the particles spaced horizontally or vertically within the fluid flow. Both orientations were evaluated for the effects of the dimensionless gap on the drag coefficient. The wake structure at higher Reynolds numbers were also evaluated for effects due to neighboring particles. A correlation was developed for the case of the horizontal particles at a dimensionless gap, L/D ≥ 2 for the range of Reynolds numbers described. The orientation effect is then studied at a fixed distance for offsets of thirty, forty-five and sixty degrees from the horizontal. Results are also presented to evaluate the effect of the diameter of a neighboring particle. The current results are restricted to the case described in the work. Future studies may build on the current work to extend the work to other effects of neighboring particles and multiple particle influence.

A soybean MADS-box protein modulates floral organ numbers, petal identity and sterility

PubMed Central

2014-01-01

Background The MADS-box transcription factors play fundamental roles in reproductive developmental control. Although the roles of many plant MADS-box proteins have been extensively studied, there are almost no functional studies of them in soybean, an important protein and oil crop in the world. In addition, the MADS-box protein orthologs may have species-specific functions. Controlling male fertility is an important goal in plant hybrid breeding but is difficult in some crops like soybean. The morphological structure of soybean flowers prevents the cross-pollination. Understanding the molecular mechanisms for floral development will aid in engineering new sterile materials that could be applied in hybrid breeding programs in soybean. Result Through microarray analysis, a flower-enriched gene in soybean was selected and designated as GmMADS28. GmMADS28 belongs to AGL9/SEP subfamily of MADS-box proteins, localized in nucleus and showed specific expression patterns in floral meristems as well as stamen and petal primordia. Expression of GmMADS28 in the stamens and petals of a soybean mutant NJS-10Hfs whose stamens are converted into petals was higher than in those of wild-type plants. Constitutive expression of GmMADS28 in tobacco promoted early flowering and converted stamens and sepals to petals. Interestingly, transgenic plants increased the numbers of sepal, petal and stamen from five to six and exhibited male sterility due to the shortened and curly filaments and the failure of pollen release from the anthers. The ectopic expression of GmMADS28 was found to be sufficient to activate expression of tobacco homologs of SOC1, LEAFY, AGL8/FUL, and DEF. In addition, we observed the interactions of GmMADS28 with soybean homologs of SOC1, AP1, and AGL8/FUL proteins. Conclusion In this study, we observed the roles of GmMADS28 in the regulation of floral organ number and petal identity. Compared to other plant AGL9/SEP proteins, GmMADS28 specifically regulates floral

A soybean MADS-box protein modulates floral organ numbers, petal identity and sterility.

PubMed

Huang, Fang; Xu, Guangli; Chi, Yingjun; Liu, Haicui; Xue, Qian; Zhao, Tuanjie; Gai, Junyi; Yu, Deyue

2014-04-02

The MADS-box transcription factors play fundamental roles in reproductive developmental control. Although the roles of many plant MADS-box proteins have been extensively studied, there are almost no functional studies of them in soybean, an important protein and oil crop in the world. In addition, the MADS-box protein orthologs may have species-specific functions. Controlling male fertility is an important goal in plant hybrid breeding but is difficult in some crops like soybean. The morphological structure of soybean flowers prevents the cross-pollination. Understanding the molecular mechanisms for floral development will aid in engineering new sterile materials that could be applied in hybrid breeding programs in soybean. Through microarray analysis, a flower-enriched gene in soybean was selected and designated as GmMADS28. GmMADS28 belongs to AGL9/SEP subfamily of MADS-box proteins, localized in nucleus and showed specific expression patterns in floral meristems as well as stamen and petal primordia. Expression of GmMADS28 in the stamens and petals of a soybean mutant NJS-10Hfs whose stamens are converted into petals was higher than in those of wild-type plants. Constitutive expression of GmMADS28 in tobacco promoted early flowering and converted stamens and sepals to petals. Interestingly, transgenic plants increased the numbers of sepal, petal and stamen from five to six and exhibited male sterility due to the shortened and curly filaments and the failure of pollen release from the anthers. The ectopic expression of GmMADS28 was found to be sufficient to activate expression of tobacco homologs of SOC1, LEAFY, AGL8/FUL, and DEF. In addition, we observed the interactions of GmMADS28 with soybean homologs of SOC1, AP1, and AGL8/FUL proteins. In this study, we observed the roles of GmMADS28 in the regulation of floral organ number and petal identity. Compared to other plant AGL9/SEP proteins, GmMADS28 specifically regulates floral organ number, filament length and

SurvExpress: an online biomarker validation tool and database for cancer gene expression data using survival analysis.

PubMed

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R.

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

PubMed Central

Aguirre-Gamboa, Raul; Gomez-Rueda, Hugo; Martínez-Ledesma, Emmanuel; Martínez-Torteya, Antonio; Chacolla-Huaringa, Rafael; Rodriguez-Barrientos, Alberto; Tamez-Peña, José G.; Treviño, Victor

2013-01-01

Validation of multi-gene biomarkers for clinical outcomes is one of the most important issues for cancer prognosis. An important source of information for virtual validation is the high number of available cancer datasets. Nevertheless, assessing the prognostic performance of a gene expression signature along datasets is a difficult task for Biologists and Physicians and also time-consuming for Statisticians and Bioinformaticians. Therefore, to facilitate performance comparisons and validations of survival biomarkers for cancer outcomes, we developed SurvExpress, a cancer-wide gene expression database with clinical outcomes and a web-based tool that provides survival analysis and risk assessment of cancer datasets. The main input of SurvExpress is only the biomarker gene list. We generated a cancer database collecting more than 20,000 samples and 130 datasets with censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. We show the utility and simplicity of SurvExpress in two biomarker applications for breast and lung cancer. Compared to other tools, SurvExpress is the largest, most versatile, and quickest free tool available. SurvExpress web can be accessed in http://bioinformatica.mty.itesm.mx/SurvExpress (a tutorial is included). The website was implemented in JSP, JavaScript, MySQL, and R. PMID:24066126

Unified approach for calculating the number of confined modes in multilayered waveguiding structures

NASA Astrophysics Data System (ADS)

Ruschin, S.; Griffel, G.; Hardy, A.; Croitoru, N.

1986-01-01

A general formalism is developed in order to find the number of modes and mode cutoff conditions in multilayer waveguiding structures. An explicit expression is presented for the number of confined modes that allows the modes to be counted without having to analyze the specific eigenvalue equation of the structure. The method is illustrated by its application to several structures: the buried layer, the directional coupler, and the three-guide symmetrical arrangement. By a suitable extension of the formalism, the number of well-confined modes is found for a four-layer structure.

Analysis of turbulent heat transfer, mass transfer, and friction in smooth tubes at high Prandtl and Schmidt numbers

NASA Technical Reports Server (NTRS)

Deissler, Robert G

1955-01-01

The expression for eddy diffusivity from a previous analysis was modified in order to account for the effect of kinematic viscosity on the turbulence in the region close to a wall. By using the modified expression, good agreement was obtained between predicted and experimental results for heat and mass transfer at Prandtl and Schmidt numbers between 0.5 and 3000. The effects of length-to-diameter ratio and of variable viscosity were also investigated for a wide range of Prandtl numbers.

Gene expression analysis of flax seed development

PubMed Central

2011-01-01

Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

Dark proteins: effect of inclusion body formation on quantification of protein expression.

PubMed

Iafolla, Marco A J; Mazumder, Mostafizur; Sardana, Vandit; Velauthapillai, Tharsan; Pannu, Karanbir; McMillen, David R

2008-09-01

Plasmid-borne gene expression systems have found wide application in the emerging fields of systems biology and synthetic biology, where plasmids are used to implement simple network architectures, either to test systems biology hypotheses about issues such as gene expression noise or as a means of exerting artificial control over a cell's dynamics. In both these cases, fluorescent proteins are commonly applied as a means of monitoring the expression of genes in the living cell, and efforts have been made to quantify protein expression levels through fluorescence intensity calibration and by monitoring the partitioning of proteins among the two daughter cells after division; such quantification is important in formulating the predictive models desired in systems and synthetic biology research. A potential pitfall of using plasmid-based gene expression systems is that the high protein levels associated with expression from plasmids can lead to the formation of inclusion bodies, insoluble aggregates of misfolded, nonfunctional proteins that will not generate fluorescence output; proteins caught in these inclusion bodies are thus "dark" to fluorescence-based detection methods. If significant numbers of proteins are incorporated into inclusion bodies rather than becoming biologically active, quantitative results obtained by fluorescent measurements will be skewed; we investigate this phenomenon here. We have created two plasmid constructs with differing average copy numbers, both incorporating an unregulated promoter (P(LtetO-1) in the absence of TetR) expressing the GFP derivative enhanced green fluorescent protein (EGFP), and inserted them into Escherichia coli bacterial cells (a common model organism for work on the dynamics of prokaryotic gene expression). We extracted the inclusion bodies, denatured them, and refolded them to render them active, obtaining a measurement of the average number of EGFP per cell locked into these aggregates; at the same time, we used

The Mental Number Line in Dyscalculia: Impaired Number Sense or Access From Symbolic Numbers?

PubMed

Lafay, Anne; St-Pierre, Marie-Catherine; Macoir, Joël

Numbers may be manipulated and represented mentally over a compressible number line oriented from left to right. According to numerous studies, one of the primary reasons for dyscalculia is related to improper understanding of the mental number line. Children with dyscalculia usually show difficulty when they have to place Arabic numbers on a physical number line. However, it remains unclear whether they have a deficit with the mental number line per se or a deficit with accessing it from nonsymbolic and/or symbolic numbers. Quebec French-speaking 8- to 9-year-old children with (24) and without (37) dyscalculia were assessed with transcoding tasks ( number-to-position and position-to-number) designed to assess the acuity of the mental number line with Arabic and spoken numbers as well as with analogic numerosities. Results showed that children with dyscalculia produced a larger percentage absolute error than children without mathematics difficulties in every task except the number-to-position transcoding task with analogic numerosities. Hence, these results suggested that children with dyscalculia do not have a general deficit of the mental number line but rather a deficit with accessing it from symbolic numbers.

Development of thermal stratification and destratification scaling concepts. Volume 2: Stratification. [tanks (containers)/tables (data)

NASA Technical Reports Server (NTRS)

Lovrich, T. N.; Schwartz, S. H.

1975-01-01

Temperature and pressure data obtained from the saturated Freon 113 PCA closed-tank stratification tests are presented. The data presented in tabular form are the test conditions, sensible heat values, and Freon 113 PCA liquid and ullage (vapor) properties. Also included, are graphical representations of the liquid bulk temperature and pressure histories, and dimensionless liquid-ullage delta-temperature profiles. Modified Grashof numbers and Fourier number-history data are also presented graphically.

Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

PubMed Central

Arts, Peer; van der Raadt, Jori; van Gestel, Sebastianus H.C.; Steehouwer, Marloes; Shendure, Jay; Hoischen, Alexander; Albers, Cornelis A.

2017-01-01

Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of ∼100 nucleotides and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. Compared with low-coverage RNA-Seq and a hybridization-based targeted RNA-Seq method, cDNA-smMIPs are a cost-effective high-throughput tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands). PMID:28474677

Natural occupation numbers in two-electron quantum rings.

PubMed

Tognetti, Vincent; Loos, Pierre-François

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

Natural occupation numbers in two-electron quantum rings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tognetti, Vincent, E-mail: vincent.tognetti@univ-rouen.fr; Loos, Pierre-François

2016-02-07

Natural orbitals (NOs) are central constituents for evaluating correlation energies through efficient approximations. Here, we report the closed-form expression of the NOs of two-electron quantum rings, which are prototypical finite-extension systems and new starting points for the development of exchange-correlation functionals in density functional theory. We also show that the natural occupation numbers for these two-electron paradigms are in general non-vanishing and follow the same power law decay as atomic and molecular two-electron systems.

g-Jitter Mixed Convective Slip Flow of Nanofluid past a Permeable Stretching Sheet Embedded in a Darcian Porous Media with Variable Viscosity

PubMed Central

Uddin, Mohammed J.; Khan, Waqar A.; Amin, Norsarahaida S.

2014-01-01

The unsteady two-dimensional laminar g-Jitter mixed convective boundary layer flow of Cu-water and Al2O3-water nanofluids past a permeable stretching sheet in a Darcian porous is studied by using an implicit finite difference numerical method with quasi-linearization technique. It is assumed that the plate is subjected to velocity and thermal slip boundary conditions. We have considered temperature dependent viscosity. The governing boundary layer equations are converted into non-similar equations using suitable transformations, before being solved numerically. The transport equations have been shown to be controlled by a number of parameters including viscosity parameter, Darcy number, nanoparticle volume fraction, Prandtl number, velocity slip, thermal slip, suction/injection and mixed convection parameters. The dimensionless velocity and temperature profiles as well as friction factor and heat transfer rates are presented graphically and discussed. It is found that the velocity reduces with velocity slip parameter for both nanofluids for fluid with both constant and variable properties. It is further found that the skin friction decreases with both Darcy number and momentum slip parameter while it increases with viscosity variation parameter. The surface temperature increases as the dimensionless time increases for both nanofluids. Nusselt numbers increase with mixed convection parameter and Darcy numbers and decreases with the momentum slip. Excellent agreement is found between the numerical results of the present paper with published results. PMID:24927277

Study of water based nanofluid flows in annular tubes using numerical simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Siadaty, Moein; Kazazi, Mohsen

2018-04-01

Convective heat transfer, entropy generation and pressure drop of two water based nanofluids (Cu-water and Al2O3-water) in horizontal annular tubes are scrutinized by means of computational fluids dynamics, response surface methodology and sensitivity analysis. First, central composite design is used to perform a series of experiments with diameter ratio, length to diameter ratio, Reynolds number and solid volume fraction. Then, CFD is used to calculate the Nusselt Number, Euler number and entropy generation. After that, RSM is applied to fit second order polynomials on responses. Finally, sensitivity analysis is conducted to manage the above mentioned parameters inside tube. Totally, 62 different cases are examined. CFD results show that Cu-water and Al2O3-water have the highest and lowest heat transfer rate, respectively. In addition, analysis of variances indicates that increase in solid volume fraction increases dimensionless pressure drop for Al2O3-water. Moreover, it has a significant negative and insignificant effects on Cu-water Nusselt and Euler numbers, respectively. Analysis of Bejan number indicates that frictional and thermal entropy generations are the dominant irreversibility in Al2O3-water and Cu-water flows, respectively. Sensitivity analysis indicates dimensionless pressure drop sensitivity to tube length for Cu-water is independent of its diameter ratio at different Reynolds numbers.

Quantifying Extrinsic Noise in Gene Expression Using the Maximum Entropy Framework

PubMed Central

Dixit, Purushottam D.

2013-01-01

We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of the gene product (mRNA or protein) by accounting for possible variations in extrinsic factors. The distribution of extrinsic factors is estimated using the maximum entropy principle. Our results show that extrinsic factors qualitatively and quantitatively affect the probability distribution of the gene product. We work out, in detail, the transcription of mRNA from a constitutively expressed promoter in Escherichia coli. We suggest that the variation in extrinsic factors may account for the observed wider-than-Poisson distribution of mRNA copy numbers. We successfully test our framework on a numerical simulation of a simple gene expression scheme that accounts for the variation in extrinsic factors. We also make falsifiable predictions, some of which are tested on previous experiments in E. coli whereas others need verification. Application of the presented framework to more complex situations is also discussed. PMID:23790383

Narcolepsy patients' blood-based miRNA expression profiling: miRNA expression differences with Pandemrix vaccination.

PubMed

Mosakhani, N; Sarhadi, V; Panula, P; Partinen, M; Knuutila, S

2017-11-01

Narcolepsy is a neurological sleep disorder characterized by excessive daytime sleepiness and nighttime sleep disturbance. Among children and adolescents vaccinated with Pandemrix vaccine in Finland and Sweden, the number of narcolepsy cases increased. Our aim was to identify miRNAs involved in narcolepsy and their association with Pandemrix vaccination. We performed global miRNA proofing by miRNA microarrays followed by RT-PCR verification on 20 narcolepsy patients (Pandemrix-associated and Pandemrix-non-associated) and 17 controls (vaccinated and non-vaccinated). Between all narcolepsy patients and controls, 11 miRNAs were differentially expressed; 17 miRNAs showed significantly differential expression between Pandemrix-non-associated narcolepsy patients and non-vaccinated healthy controls. MiR-188-5p and miR-4499 were over-expressed in narcolepsy patients vs healthy controls. Two miRNAs, miR-1470 and miR-4455, were under-expressed in Pandemrix-associated narcolepsy patients vs Pandemrix-non-associated narcolepsy patients. We identified miRNA expression patterns in narcolepsy patients that linked them to mRNA targets known to be involved in brain-related pathways or brain disorders. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Numerical investigation of potential stratification caused by a cryogenic helium spill inside a tunnel

NASA Astrophysics Data System (ADS)

Sinclair, Cameron; Malecha, Ziemowit; Jedrusyna, Artur

2018-04-01

The sudden release of cryogenic fluid into an accelerator tunnel can pose a significant health and safety risk. For this reason, it is important to evaluate the consequences of such a spill. Previous publications concentrated on either Oxygen Deficiency Hazard or the evaluation of mathematical models using experimental data. No studies to date have focussed on the influence of cryogen inlet conditions on flow development. In this paper, the stratification behaviour of low-temperature helium released into an air-filled accelerator tunnel is investigated for varying helium inlet diameters. A numerical model was constructed using the OpenFOAM Toolbox of a generalised 3D geometry, with similar hydraulic characteristics to the CERN and SLAC tunnels. This model has been validated against published experimental and numerical data. A dimensionless parameter, based on Bakke number, was then determined for the onset of stratification, taking into account the helium inlet diameter; a dimensionless parameter for the degree of stratification was also employed. The simulated flow behaviour is described in terms of these dimensionless parameters, as well as the temperature and oxygen concentration at various heights throughout the tunnel.

Generalization of experimental data on heat transfer in permeable shells made of porous reticular materials

NASA Astrophysics Data System (ADS)

Polyakov, A. F.; Strat'ev, V. K.; Tret'yakov, A. F.; Shekhter, Yu. L.

2010-06-01

Heat transfer from six samples of porous reticular material to cooling gas (air) at small Reynolds numbers is experimentally studied. The specific features pertinent to heat transfer essentially affected by longitudinal heat conductivity along gas flow are analyzed. The experimental results are generalized in the form of dimensionless empirical relations.

The network level reproduction number for infectious diseases with both vertical and horizontal transmission.

PubMed

Xue, Ling; Scoglio, Caterina

2013-05-01

A wide range of infectious diseases are both vertically and horizontally transmitted. Such diseases are spatially transmitted via multiple species in heterogeneous environments, typically described by complex meta-population models. The reproduction number, R0, is a critical metric predicting whether the disease can invade the meta-population system. This paper presents the reproduction number for a generic disease vertically and horizontally transmitted among multiple species in heterogeneous networks, where nodes are locations, and links reflect outgoing or incoming movement flows. The metapopulation model for vertically and horizontally transmitted diseases is gradually formulated from two species, two-node network models. We derived an explicit expression of R0, which is the spectral radius of a matrix reduced in size with respect to the original next generation matrix. The reproduction number is shown to be a function of vertical and horizontal transmission parameters, and the lower bound is the reproduction number for horizontal transmission. As an application, the reproduction number and its bounds for the Rift Valley fever zoonosis, where livestock, mosquitoes, and humans are the involved species are derived. By computing the reproduction number for different scenarios through numerical simulations, we found the reproduction number is affected by livestock movement rates only when parameters are heterogeneous across nodes. To summarize, our study contributes the reproduction number for vertically and horizontally transmitted diseases in heterogeneous networks. This explicit expression is easily adaptable to specific infectious diseases, affording insights into disease evolution. Copyright © 2013 Elsevier Inc. All rights reserved.

Cysteinyl Leukotriene 1 Receptor Expression Associated With Bronchial Inflammation in Severe Exacerbations of COPD

PubMed Central

Zhu, Jie; Bandi, Venkata; Qiu, Shengyang; Figueroa, David J.; Evans, Jilly F.; Barnes, Neil; Guntupalli, Kay K.

2012-01-01

Background: Cysteinyl leukotriene 1 (CysLT1) receptor expression is known to be increased in the airway mucosa of patients with asthma, especially during exacerbations; however, nothing is known of its expression in COPD. Methods: We applied immunohistochemistry and in situ hybridization to endobronchial biopsies to determine inflammatory cell CysLT1 receptor protein and mRNA expression in the following: (1) 15 nonsmoker control subjects (NSC), (2) 16 smokers with moderate to severe COPD in its stable phase (S-COPD), and (3) 15 smokers with COPD hospitalized for a severe exacerbation (SE-COPD). Results: The total number of bronchial mucosal inflammatory cells (CD45+) and those expressing CysLT1 receptor protein were significantly greater in SE-COPD (CysLT1 receptor protein: median [range] = 139 [31-634]) as compared with S-COPD (32 [6-114]) or NSC (16 [4-66]) (P < .001 for both). CysLT1 receptor gene expression showed similar differences. A greater proportion of CD451 cells expressed CysLT1 receptor protein in SE-COPD (median [range] = 22% [8-81]) compared with S-COPD (10% [4-32]) (P < .03) or NSC (7% [1-19]) (P < .002). In SE-COPD, the relative frequencies of CysLT1 receptor-expressing cells were as follows: tryptase1 mast cells > CD681 monocytes/macrophage > neutrophils > CD201 B lymphocytes = EG21 eosinophils. Moreover, there were positive correlations between the numbers of cells expressing CysLT1 receptor protein and the numbers of CD451 cells (r = 0.78; P < .003) and tryptase1 mast cells (r = 0.62; P < .02). Conclusions: Bronchial mucosal CysLT1 receptor-positive inflammatory cells are present in the bronchial mucosa in COPD in greatest number in those experiencing a severe exacerbation. PMID:22871757

Cancer-testis antigen expression is shared between epithelial ovarian cancer tumors.

PubMed

Garcia-Soto, Arlene E; Schreiber, Taylor; Strbo, Natasa; Ganjei-Azar, Parvin; Miao, Feng; Koru-Sengul, Tulay; Simpkins, Fiona; Nieves-Neira, Wilberto; Lucci, Joseph; Podack, Eckhard R

2017-06-01

Cancer-testis (CT) antigens have been proposed as potential targets for cancer immunotherapy. Our objective was to evaluate the expression of a panel of CT antigens in epithelial ovarian cancer (EOC) tumor specimens, and to determine if antigen sharing occurs between tumors. RNA was isolated from EOC tumor specimens, EOC cell lines and benign ovarian tissue specimens. Real time-PCR analysis was performed to determine the expression level of 20 CT antigens. A total of 62 EOC specimens, 8 ovarian cancer cell lines and 3 benign ovarian tissues were evaluated for CT antigen expression. The majority of the specimens were: high grade (62%), serous (68%) and advanced stage (74%). 58 (95%) of the EOC tumors analyzed expressed at least one of the CT antigens evaluated. The mean number of CT antigen expressed was 4.5 (0-17). The most frequently expressed CT antigen was MAGE A4 (65%). Antigen sharing analysis showed the following: 9 tumors shared only one antigen with 62% of the evaluated specimens, while 37 tumors shared 4 or more antigens with 82%. 5 tumors expressed over 10 CT antigens, which were shared with 90% of the tumor panel. CT antigens are expressed in 95% of EOC tumor specimens. However, not a single antigen was universally expressed across all samples. The degree of antigen sharing between tumors increased with the total number of antigens expressed. These data suggest a multi-epitope approach for development of immunotherapy for ovarian cancer treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Gene Expression Profiling of Gastric Cancer

PubMed Central

Marimuthu, Arivusudar; Jacob, Harrys K.C.; Jakharia, Aniruddha; Subbannayya, Yashwanth; Keerthikumar, Shivakumar; Kashyap, Manoj Kumar; Goel, Renu; Balakrishnan, Lavanya; Dwivedi, Sutopa; Pathare, Swapnali; Dikshit, Jyoti Bajpai; Maharudraiah, Jagadeesha; Singh, Sujay; Sameer Kumar, Ghantasala S; Vijayakumar, M.; Veerendra Kumar, Kariyanakatte Veeraiah; Premalatha, Chennagiri Shrinivasamurthy; Tata, Pramila; Hariharan, Ramesh; Roa, Juan Carlos; Prasad, T.S.K; Chaerkady, Raghothama; Kumar, Rekha Vijay; Pandey, Akhilesh

2015-01-01

Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent’s whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma. PMID:27030788

Enhanced transgene expression in rice following selection controlled by weak promoters.

PubMed

Zhou, Jie; Yang, Yong; Wang, Xuming; Yu, Feibo; Yu, Chulang; Chen, Juan; Cheng, Ye; Yan, Chenqi; Chen, Jianping

2013-03-27

Techniques that enable high levels of transgene expression in plants are attractive for the commercial production of plant-made recombinant pharmaceutical proteins or other gene transfer related strategies. The conventional way to increase the yield of desired transgenic products is to use strong promoters to control the expression of the transgene. Although many such promoters have been identified and characterized, the increase obtainable from a single promoter is ultimately limited to a certain extent. In this study, we report a method to magnify the effect of a single promoter by using a weak promoter-based selection system in transgenic rice. tCUP1, a fragment derived from the tobacco cryptic promoter (tCUP), was tested for its activity in rice by fusion to both a β-glucuronidase (GUS) reporter and a hygromycin phosphotransferase (HPT) selectable marker. The tCUP1 promoter allowed the recovery of transformed rice plants and conferred tissue specific expression of the GUS reporter, but was much weaker than the CaMV 35S promoter in driving a selectable marker for growth of resistant calli. However, in the resistant calli and regenerated transgenic plants selected by the use of tCUP1, the constitutive expression of green fluorescent protein (GFP) was dramatically increased as a result of the additive effect of multiple T-DNA insertions. The correlation between attenuated selection by a weak promoter and elevation of copy number and foreign gene expression was confirmed by using another relatively weak promoter from nopaline synthase (Nos). The use of weak promoter derived selectable markers leads to a high T-DNA copy number and then greatly increases the expression of the foreign gene. The method described here provides an effective approach to robustly enhance the expression of heterogenous transgenes through copy number manipulation in rice.

Activated microglia proliferate at neurites of mutant huntingtin-expressing neurons

PubMed Central

Kraft, Andrew D.; Kaltenbach, Linda S.; Lo, Donald C.; Harry, G. Jean

2011-01-01

In Huntington's disease (HD), mutated huntingtin (mhtt) causes striatal neurodegeneration which is paralleled by elevated microglia cell numbers. In vitro cortico-striatal slice and primary neuronal culture models, in which neuronal expression of mhtt fragments drives HD-like neurotoxicity, were employed to examine wild type microglia during both the initiation and progression of neuronal pathology. As neuronal pathology progressed, microglia initially localized in the vicinity of neurons expressing mhtt fragments increased in number, demonstrated morphological evidence of activation, and expressed the proliferation marker, Ki67. These microglia were positioned along irregular neurites, but did not localize with mhtt inclusions nor exacerbate mhtt fragment-induced neurotoxicity. Prior to neuronal pathology, microglia upregulated Iba1, signaling a functional shift. With neurodegeneration, interleukin-6 and complement component 1q were increased. The results suggest a stimulatory, proliferative signal for microglia present at the onset of mhtt fragment-induced neurodegeneration. Thus, microglia effect a localized inflammatory response to neuronal mhtt expression that may serve to direct microglial removal of dysfunctional neurites or aberrant synapses, as is required for reparative actions in vivo. PMID:21482444

Number needed to sacrifice: statistical taboo or decision-making tool?

PubMed

Trewby, Peter

2013-03-01

The percentage that benefit from medical preventive measures is small but all are exposed to the risk of side effects so most of those harmed would never benefit from their use. There is no expression or acronym to describe the ratio of harm to benefit nor discussion of what level of harm is acceptable for what benefit. Here we describe the harm to benefit ratio (HBR) expressed as number harmed (H) for 100 to benefit (B) and calculated for commonly used medical interventions. For post TIA carotid endarterectomy the HBR is 25 (25 postoperative strokes or deaths are caused for 100 to be stroke free at 5 years); warfarin in atrial fibrillation in patients aged under 65 results in 400 intracerebral haemorrhages for every 100 saved from a thromboembolic event; fibrinolytic treatment for stroke causes 44 symptomatic intracranial haemorrhages for every 100 that have minimal disability at 3 months; aspirin in high risk patients causes 33 major bleeds for every 100 occlusive vascular events prevented; routine inpatient thromboprophylaxis causes 133 additional bleeds for every 100 pulmonary emboli prevented; breast cancer screening causes 1000 unnecessary cancer treatments for 100 cancer deaths to be prevented. The HBR or number needed to sacrifice is larger than most imagine. Its wider use would allow us better to recognise the number harmed, allow better informed consent, compare different preventive strategies and understand the risks as well as benefits of preventive treatments.

Techniques for simulating flood hydrographs and estimating flood volumes for ungaged basins in east and west Tennessee

USGS Publications Warehouse

Gamble, C.R.

1989-01-01

A dimensionless hydrograph developed for a variety of basin conditions in Georgia was tested for its applicability to streams in East and West Tennessee by comparing it to a similar dimensionless hydrograph developed for streams in East and West Tennessee. Hydrographs of observed discharge at 83 streams in East Tennessee and 38 in West Tennessee were used in the study. Statistical analyses were performed by comparing simulated (or computed) hydrographs, derived by application of the Georgia dimensionless hydrograph, and dimensionless hydrographs developed from Tennessee data, with the observed hydrographs at 50 and 75% of their peak-flow widths. Results of the tests indicate that the Georgia dimensionless hydrography is virtually the same as the one developed for streams in East Tennessee, but that it is different from the dimensionless hydrograph developed for streams in West Tennessee. Because of the extensive testing of the Georgia dimensionless hydrograph, it was determined to be applicable for East Tennessee, whereas the dimensionless hydrograph developed from data on streams in West Tennessee was determined to be applicable in West Tennessee. As part of the dimensionless hydrograph development, an average lagtime in hours for each study basin, and the volume in inches of flood runoff for each flood event were computed. By use of multiple-regression analysis, equations were developed that relate basin lagtime to drainage area size, basin length, and percent impervious area. Similarly, flood volumes were related to drainage area size, peak discharge, and basin lagtime. These equations, along with the appropriate dimensionless hydrograph, can be used to estimate a typical (average) flood hydrograph and volume for recurrence-intervals up to 100 years at any ungaged site draining less than 50 sq mi in East and West Tennessee. (USGS)

Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro.

PubMed

de Souza, Alessandra A; Takita, Marco A; Coletta-Filho, Helvécio D; Caldana, Camila; Yanai, Giane M; Muto, Nair H; de Oliveira, Regina C; Nunes, Luiz R; Machado, Marcos A

2004-08-15

A biofilm is a community of microorganisms attached to a solid surface. Cells within biofilms differ from planktonic cells, showing higher resistance to biocides, detergent, antibiotic treatments and host defense responses. Even though there are a number of gene expression studies in bacterial biofilm formation, limited information is available concerning plant pathogen. It was previously demonstrated that the plant pathogen Xylella fastidiosa could grow as a biofilm, a possibly important factor for its pathogenicity. In this study we utilized analysis of microarrays to specifically identify genes expressed in X. fastidiosa cells growing in a biofilm, when compared to planktonic cells. About half of the differentially expressed genes encode hypothetical proteins, reflecting the large number of ORFs with unknown functions in bacterial genomes. However, under the biofilm condition we observed an increase in the expression of some housekeeping genes responsible for metabolic functions. We also found a large number of genes from the pXF51 plasmid being differentially expressed. Some of the overexpressed genes in the biofilm condition encode proteins involved in attachment to surfaces. Other genes possibly confer advantages to the bacterium in the environment that it colonizes. This study demonstrates that the gene expression in the biofilm growth condition of the plant pathogen X. fastidiosa is quite similar to other characterized systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mériaux, C. A., E-mail: cameriaux@fc.ul.pt; Kurz-Besson, C. B.; Zemach, T.

In this study, we investigate the motion of particulate gravity currents in a horizontal V-shaped channel. The particulate currents consisted of particles whose size varied between 0 and 100 μm but whose mean size increased. Particles were poorly sorted as the variance of the grain size distributions varied between 50 and 200. While the phases of propagation of homogeneous currents in such a geometry have been studied in the literature, this study considers the effects of the grain size on the propagation. The distance of propagation and front velocity of full-depth high-Reynolds-number lock-release experiments and shallow-water equation simulations were analyzedmore » as the mean grain size of the initial particle distributions, defined by mass, was increased from 19 to 58 μm. Similar to the homogeneous currents, three consecutive phases of the front velocity could be identified but their characteristics and extent depend on the particle size. The initial phase, in particular, depends on a dimensionless settling number β that is defined as the ratio of two characteristic time scales, the propagation time x{sub 0}/U, where U is the scale for the front speed and x{sub 0} the lock length, and the settling time h{sub 0}/v{sub s}, where v{sub s} is the scale for the settling velocity and h{sub 0} the initial height of the current. For dimensionless settling numbers less than 0.001, the initial phase is characterized by a constant velocity for over about 6-7 lock lengths that is alike the initial slumping phase of perfectly constant velocity of the homogeneous currents. For dimensionless settling numbers greater than 0.001 and less than 0.015, the initial phase is no longer characterized by a constant velocity but an almost constant velocity for over about a similar 6-7 lock lengths. For dimensionless settling numbers greater than 0.015, however, as such, this phase is no longer seen. This initial phase is followed by a continuous decrease of the front advance

Ikaros gene expression and leukemia.

PubMed

Tonnelle, Cécile; Calmels, Boris; Maroc, Christine; Gabert, Jean; Chabannon, Christian

2002-01-01

The Ikaros (Ik) protein, or LyF1, was initially described as a protein binding to regulatory sequences of a number of genes expressed in murine lymphoid cells. Ikaros is a critical regulator of normal hematopoietic stem cell differentiation, as evidenced by dramatic defects in the lymphoid compartments, in homozygous animals with gene inactivation. Because differential splicing produces multiple isoforms with potentially different functions, Ikaros provides a unique model to study how post-transcriptional mechanisms may be involved in neoplastic processes. Indeed, several groups including ours have underlined evidences that expression of different Ikaros isoforms vary among different types of leukemias. The predominance of short isoforms in certain subsets is intriguing. Here, additional observations reinforced the hypothesis that Ikaros expression may be deregulated in human leukemias. Whether this is a cause or a consequence of the leukemic process remains speculative. Other human diseases however, provide examples of abnormal post-transcriptional regulations that have been further characterized.

Recombinant Expression Screening of P. aeruginosa Bacterial Inner Membrane Proteins

PubMed Central

2010-01-01

Background Transmembrane proteins (TM proteins) make up 25% of all proteins and play key roles in many diseases and normal physiological processes. However, much less is known about their structures and molecular mechanisms than for soluble proteins. Problems in expression, solubilization, purification, and crystallization cause bottlenecks in the characterization of TM proteins. This project addressed the need for improved methods for obtaining sufficient amounts of TM proteins for determining their structures and molecular mechanisms. Results Plasmid clones were obtained that encode eighty-seven transmembrane proteins with varying physical characteristics, for example, the number of predicted transmembrane helices, molecular weight, and grand average hydrophobicity (GRAVY). All the target proteins were from P. aeruginosa, a gram negative bacterial opportunistic pathogen that causes serious lung infections in people with cystic fibrosis. The relative expression levels of the transmembrane proteins were measured under several culture growth conditions. The use of E. coli strains, a T7 promoter, and a 6-histidine C-terminal affinity tag resulted in the expression of 61 out of 87 test proteins (70%). In this study, proteins with a higher grand average hydrophobicity and more transmembrane helices were expressed less well than less hydrophobic proteins with fewer transmembrane helices. Conclusions In this study, factors related to overall hydrophobicity and the number of predicted transmembrane helices correlated with the relative expression levels of the target proteins. Identifying physical characteristics that correlate with protein expression might aid in selecting the "low hanging fruit", or proteins that can be expressed to sufficient levels using an E. coli expression system. The use of other expression strategies or host species might be needed for sufficient levels of expression of transmembrane proteins with other physical characteristics. Surveys like this

Quantification of multiple gene expression in individual cells.

PubMed

Peixoto, António; Monteiro, Marta; Rocha, Benedita; Veiga-Fernandes, Henrique

2004-10-01

Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. So far, these assessments can only be performed at the population level. Therefore, they determine the average gene expression within a population, overlooking possible cell-to-cell heterogeneity that could lead to different cell behaviors/cell fates. Understanding individual cell behavior requires multiple gene expression analyses of single cells, and may be fundamental for the understanding of all types of biological events and/or differentiation processes. We here describe a new reverse transcription-polymerase chain reaction (RT-PCR) approach allowing the simultaneous quantification of the expression of 20 genes in the same single cell. This method has broad application, in different species and any type of gene combination. RT efficiency is evaluated. Uniform and maximized amplification conditions for all genes are provided. Abundance relationships are maintained, allowing the precise quantification of the absolute number of mRNA molecules per cell, ranging from 2 to 1.28 x 10(9) for each individual gene. We evaluated the impact of this approach on functional genetic read-outs by studying an apparently homogeneous population (monoclonal T cells recovered 4 d after antigen stimulation), using either this method or conventional real-time RT-PCR. Single-cell studies revealed considerable cell-to-cell variation: All T cells did not express all individual genes. Gene coexpression patterns were very heterogeneous. mRNA copy numbers varied between different transcripts and in different cells. As a consequence, this single-cell assay introduces new and fundamental information regarding functional genomic read-outs. By comparison, we also show that conventional quantitative assays determining population averages supply insufficient information, and may even be highly misleading.

Symposium on Naval Hydrodynamics (10th), Hydrodynamics for Safety Fundamental Hydrodynamics

DTIC Science & Technology

1974-01-01

vessel, and certain controlled conditions. The numerical particularly the rudder, operates in the wake of investigation also shows that the experimental ...expressed in terms of dimensionless quantities N1,Y1, and XV The following rudder control .aeacteristics are based on non -dimenslonalizing parometers p...the waves begin to build extensive experimental programs would be in the second wave group . The mraximum required to adequately describe the rtarboard

Beta-defensin genomic copy number is not a modifier locus for cystic fibrosis

PubMed Central

Hollox, Edward J; Davies, Jane; Griesenbach, Uta; Burgess, Juliana; Alton, Eric WFW; Armour, John AL

2005-01-01

Human beta-defensin 2 (DEFB4, also known as DEFB2 or hBD-2) is a salt-sensitive antimicrobial protein that is expressed in lung epithelia. Previous work has shown that it is encoded in a cluster of beta-defensin genes at 8p23.1, which varies in copy number between 2 and 12 in different individuals. We determined the copy number of this locus in 355 patients with cystic fibrosis (CF), and tested for correlation between beta-defensin cluster genomic copy number and lung disease associated with CF. No significant association was found. PMID:16336654

Regionalization of precipitation characteristics in Montana using L-moments

USGS Publications Warehouse

Parrett, C.

1998-01-01

Dimensionless precipitation-frequency curves for estimating precipitation depths having small exceedance probabilities were developed for 2-, 6-, and 24-hour storm durations for three homogeneous regions in Montana. L-moment statistics were used to help define the homogeneous regions. The generalized extreme value distribution was used to construct the frequency curves for each duration within each region. The effective record length for each duration in each region was estimated using a graphical method and was found to range from 500 years for 6-hour duration data in Region 2 to 5,100 years for 24-hour duration data in Region 3. The temporal characteristics of storms were analyzed, and methods for estimating synthetic storm hyetographs were developed. Dimensionless depth-duration data were grouped by independent duration (2,6, and 24 hours) and by region, and the beta distribution was fit to dimensionless depth data for various incremental time intervals. Ordinary least-squares regression was used to develop relations between dimensionless depths for a key, short duration - termed the kernel duration - and dimensionless depths for other durations. The regression relations were used, together with the probabilistic dimensionless depth data for the kernel duration, to calculate dimensionless depth-duration curves for exceedance probabilities from .1 to .9. Dimensionless storm hyetographs for each independent duration in each region were constructed for median value conditions based on an exceedance probability of .5.

Effect of arachidonic acid metabolites on CR1 expression by B-lymphocytes.

PubMed

Cook, J M; Guibert, F; Delebassee, S; Gualde, N

1989-01-01

The effect of arachidonic acid metabolites on the expression of the receptor for the C3b/C4b fragment of complement (CR1) by human B-lymphocytes was investigated. Kinetic experiments to determine CR1 expression over time indicated that the maximal receptor number occurred at 2 h, followed by a return to baseline values. Addition of 10(-4) M puromycin to the cells suggested that the increase was due to the expression of an intracellular pool and not de novo synthesis of new receptor molecules. B-lymphocytes were incubated with arachidonic acid, 15-hydroxyeicosatetraenoic acid, leukotrienes B4 or C4 or prostaglandin E2 (PGE2). The quantity of membrane antigenic binding sites was determined before and after incubation. The lipoxygenase metabolites did not alter CR1 numbers. In contrast, PGE2 significantly decreased (P less than 0.05) the quantity of CR1 expressed. In kinetic experiments, PGE2 blocked the maximal expression of CR1 seen at 2 h, indicating that it prevents the appearance of an intracellular pool of receptor. These results show that CR1 number on B-lymphocytes can be altered by at least one arachidonic acid metabolite. This may offer a partial explanation for the inhibitory effects of PGE2 on B-cell proliferation and immunoglobulin secretion since CR1 is implicated in B-lymphocyte differentiation and specific antibody response.

Sex-Biased Gene Expression and Sexual Conflict throughout Development

PubMed Central

Ingleby, Fiona C.; Flis, Ilona; Morrow, Edward H.

2015-01-01

Sex-biased gene expression is likely to account for most sexually dimorphic traits because males and females share much of their genome. When fitness optima differ between sexes for a shared trait, sexual dimorphism can allow each sex to express their optimum trait phenotype, and in this way, the evolution of sex-biased gene expression is one mechanism that could help to resolve intralocus sexual conflict. Genome-wide patterns of sex-biased gene expression have been identified in a number of studies, which we review here. However, very little is known about how sex-biased gene expression relates to sex-specific fitness and about how sex-biased gene expression and conflict vary throughout development or across different genotypes, populations, and environments. We discuss the importance of these neglected areas of research and use data from a small-scale experiment on sex-specific expression of genes throughout development to highlight potentially interesting avenues for future research. PMID:25376837

Rotating thermal convection at very large Rayleigh numbers

NASA Astrophysics Data System (ADS)

Weiss, Stephan; van Gils, Dennis; Ahlers, Guenter; Bodenschatz, Eberhard

2016-11-01

The large scale thermal convection systems in geo- and astrophysics are usually influenced by Coriolis forces caused by the rotation of their celestial bodies. To better understand the influence of rotation on the convective flow field and the heat transport at these conditions, we study Rayleigh-Bénard convection, using pressurized sulfur hexaflouride (SF6) at up to 19 bars in a cylinder of diameter D=1.12 m and a height of L=2.24 m. The gas is heated from below and cooled from above and the convection cell sits on a rotating table inside a large pressure vessel (the "Uboot of Göttingen"). With this setup Rayleigh numbers of up to Ra =1015 can be reached, while Ekman numbers as low as Ek =10-8 are possible. The Prandtl number in these experiment is kept constant at Pr = 0 . 8 . We report on heat flux measurements (expressed by the Nusselt number Nu) as well as measurements from more than 150 temperature probes inside the flow. We thank the Deutsche Forschungsgemeinschaft (DFG) for financial support through SFB963: "Astrophysical Flow Instabilities and Turbulence". The work of GA was supported in part by the US National Science Foundation through Grant DMR11-58514.

Integrating Tenascin-C protein expression and 1q25 copy number status in pediatric intracranial ependymoma prognostication: A new model for risk stratification.

PubMed

Andreiuolo, Felipe; Le Teuff, Gwénaël; Bayar, Mohamed Amine; Kilday, John-Paul; Pietsch, Torsten; von Bueren, André O; Witt, Hendrik; Korshunov, Andrey; Modena, Piergiorgio; Pfister, Stefan M; Pagès, Mélanie; Castel, David; Giangaspero, Felice; Chimelli, Leila; Varlet, Pascale; Rutkowski, Stefan; Frappaz, Didier; Massimino, Maura; Grundy, Richard; Grill, Jacques

2017-01-01

Despite multimodal therapy, prognosis of pediatric intracranial ependymomas remains poor with a 5-year survival rate below 70% and frequent late deaths. This multicentric European study evaluated putative prognostic biomarkers. Tenascin-C (TNC) immunohistochemical expression and copy number status of 1q25 were retained for a pooled analysis of 5 independent cohorts. The prognostic value of TNC and 1q25 on the overall survival (OS) was assessed using a Cox model adjusted to age at diagnosis, tumor location, WHO grade, extent of resection, radiotherapy and stratified by cohort. Stratification on a predictor that did not satisfy the proportional hazards assumption was considered. Model performance was evaluated and an internal-external cross validation was performed. Among complete cases with 5-year median follow-up (n = 470; 131 deaths), TNC and 1q25 gain were significantly associated with age at diagnosis and posterior fossa tumor location. 1q25 status added independent prognostic value for death beyond the classical variables with a hazard ratio (HR) = 2.19 95%CI = [1.29; 3.76] (p = 0.004), while TNC prognostic relation was tumor location-dependent with HR = 2.19 95%CI = [1.29; 3.76] (p = 0.004) in posterior fossa and HR = 0.64 [0.28; 1.48] (p = 0.295) in supratentorial (interaction p value = 0.015). The derived prognostic score identified 3 different robust risk groups. The omission of upfront RT was not associated with OS for good and intermediate prognostic groups while the absence of upfront RT was negatively associated with OS in the poor risk group. Integrated TNC expression and 1q25 status are useful to better stratify patients and to eventually adapt treatment regimens in pediatric intracranial ependymoma.

Serial analysis of gene expression in the silkworm, Bombyx mori.

PubMed

Huang, Jianhua; Miao, Xuexia; Jin, Weirong; Couble, Pierre; Mita, Kasuei; Zhang, Yong; Liu, Wenbin; Zhuang, Leijun; Shen, Yan; Keime, Celine; Gandrillon, Olivier; Brouilly, Patrick; Briolay, Jerome; Zhao, Guoping; Huang, Yongping

2005-08-01

The silkworm Bombyx mori is one of the most economically important insects and serves as a model for Lepidoptera insects. We used serial analysis of gene expression (SAGE) to derive profiles of expressed genes during the developmental life cycle of the silkworm and to create a reference for understanding silkworm metamorphosis. We generated four SAGE libraries, one from each of the four developmental stages of the silkworm. In total we obtained 257,964 SAGE tags, of which 39,485 were unique tags. Sorted by copy number, 14.1% of the unique tags were detected at a median to high level (five or more copies), 24.2% at lower levels (two to four copies), and 61.7% as single copies. Using a basic local alignment search tool on the EST database, 35% of the tags matched known silkworm expressed sequence tags. SAGE demonstrated that a number of the genes were up- or down-regulated during the four developmental phases of the egg, larva, pupa, and adult. Furthermore, we found that the generation of longer cDNA fragments from SAGE tags constituted the most efficient method of gene identification, which facilitated the analysis of a large number of unknown genes.

Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 4; Acquire TM-Data for Type A and Type B Sensors for "Express-A" Number 3 Satellite, Task 27A

NASA Technical Reports Server (NTRS)

Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

2003-01-01

This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E., and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

Paint-by-Numbers Music.

ERIC Educational Resources Information Center

Haack, Paul

1982-01-01

Discusses how to teach the expressive aspects of music more effectively. For example, teachers can use verbal imagery to communicate how music is expressive of the human condition. Students should be encouraged to experiment with the possibilities of musical expression and allowed to choose their own mode of expression. (AM)

Quantitative analysis of lentiviral transgene expression in mice over seven generations.

PubMed

Wang, Yong; Song, Yong-tao; Liu, Qin; Liu, Cang'e; Wang, Lu-lu; Liu, Yu; Zhou, Xiao-yang; Wu, Jun; Wei, Hong

2010-10-01

Lentiviral transgenesis is now recognized as an extremely efficient and cost-effective method to produce transgenic animals. Transgenes delivered by lentiviral vectors exhibited inheritable expression in many species including those which are refractory to genetic modification such as non-human primates. However, epigenetic modification was frequently observed in lentiviral integrants, and transgene expression found to be inversely correlated with methylation density. Recent data showed that about one-third lentiviral integrants exhibited hypermethylation and low expression, but did not demonstrate whether those integrants with high expression could remain constant expression and hypomethylated during long term germline transmission. In this study, using lentiviral eGFP transgenic mice as the experimental animals, lentiviral eGFP expression levels and its integrant numbers in genome were quantitatively analyzed by fluorescent quantitative polymerase-chain reaction (FQ-PCR), using the house-keeping gene ribosomal protein S18 (Rps18) and the single copy gene fatty acid binding protein of the intestine (Fabpi) as the internal controls respectively. The methylation densities of the integrants were quantitatively analyzed by bisulfite sequencing. We found that the lentiviral integrants with high expression exhibited a relative constant expression level per integrant over at least seven generations. Besides, the individuals containing these integrants exhibited eGFP expression levels which were positively and almost linearly correlated with the integrant numbers in their genomes, suggesting that no remarkable position effect on transgene expression of the integrants analyzed was observed. In addition, over seven generations the methylation density of these integrants did not increase, but rather decreased remarkably, indicating that these high expressing integrants were not subjected to de novo methylation during at least seven generations of germline transmission. Taken

Mutations That Stimulate flhDC Expression in Escherichia coli K-12.

PubMed

Fahrner, Karen A; Berg, Howard C

2015-10-01

Motility is a beneficial attribute that enables cells to access and explore new environments and to escape detrimental ones. The organelle of motility in Escherichia coli is the flagellum, and its production is initiated by the activating transcription factors FlhD and FlhC. The expression of these factors by the flhDC operon is highly regulated and influenced by environmental conditions. The flhDC promoter is recognized by σ(70) and is dependent on the transcriptional activator cyclic AMP (cAMP)-cAMP receptor protein complex (cAMP-CRP). A number of K-12 strains exhibit limited motility due to low expression levels of flhDC. We report here a large number of mutations that stimulate flhDC expression in such strains. They include single nucleotide changes in the -10 element of the promoter, in the promoter spacer, and in the cAMP-CRP binding region. In addition, we show that insertion sequence (IS) elements or a kanamycin gene located hundreds of base pairs upstream of the promoter can effectively enhance transcription, suggesting that the topology of a large upstream region plays a significant role in the regulation of flhDC expression. None of the mutations eliminated the requirement for cAMP-CRP for activation. However, several mutations allowed expression in the absence of the nucleoid organizing protein, H-NS, which is normally required for flhDC expression. The flhDC operon of Escherichia coli encodes transcription factors that initiate flagellar synthesis, an energetically costly process that is highly regulated. Few deregulating mutations have been reported thus far. This paper describes new single nucleotide mutations that stimulate flhDC expression, including a number that map to the promoter spacer region. In addition, this work shows that insertion sequence elements or a kanamycin gene located far upstream from the promoter or repressor binding sites also stimulate transcription, indicating a role of regional topology in the regulation of flh

The electric field in capacitively coupled RF discharges: a smooth step model that includes thermal and dynamic effects

NASA Astrophysics Data System (ADS)

Brinkmann, Ralf Peter

2015-12-01

The electric field in radio-frequency driven capacitively coupled plasmas (RF-CCP) is studied, taking thermal (finite electron temperature) and dynamic (finite electron mass) effects into account. Two dimensionless numbers are introduced, the ratios ε ={λ\\text{D}}/l of the electron Debye length {λ\\text{D}} to the minimum plasma gradient length l (typically the sheath thickness) and η ={ω\\text{RF}}/{ω\\text{pe}} of the RF frequency {ω\\text{RF}} to the electron plasma frequency {ω\\text{pe}} . Assuming both numbers small but finite, an asymptotic expansion of an electron fluid model is carried out up to quadratic order inclusively. An expression for the electric field is obtained which yields (i) the space charge field in the sheath, (ii) the generalized Ohmic and ambipolar field in the plasma, and (iii) a smooth interpolation for the transition in between. The new expression is a direct generalization of the Advanced Algebraic Approximation (AAA) proposed by the same author (2009 J. Phys. D: Appl. Phys. 42 194009), which can be recovered for η \\to 0 , and of the established Step Model (SM) by Godyak (1976 Sov. J. Plasma Phys. 2 78), which corresponds to the simultaneous limits η \\to 0 , ε \\to 0 . A comparison of the hereby proposed Smooth Step Model (SSM) with a numerical solution of the full dynamic problem proves very satisfactory.

Perceptual integration of kinematic components in the recognition of emotional facial expressions.

PubMed

Chiovetto, Enrico; Curio, Cristóbal; Endres, Dominik; Giese, Martin

2018-04-01

According to a long-standing hypothesis in motor control, complex body motion is organized in terms of movement primitives, reducing massively the dimensionality of the underlying control problems. For body movements, this low-dimensional organization has been convincingly demonstrated by the learning of low-dimensional representations from kinematic and EMG data. In contrast, the effective dimensionality of dynamic facial expressions is unknown, and dominant analysis approaches have been based on heuristically defined facial "action units," which reflect contributions of individual face muscles. We determined the effective dimensionality of dynamic facial expressions by learning of a low-dimensional model from 11 facial expressions. We found an amazingly low dimensionality with only two movement primitives being sufficient to simulate these dynamic expressions with high accuracy. This low dimensionality is confirmed statistically, by Bayesian model comparison of models with different numbers of primitives, and by a psychophysical experiment that demonstrates that expressions, simulated with only two primitives, are indistinguishable from natural ones. In addition, we find statistically optimal integration of the emotion information specified by these primitives in visual perception. Taken together, our results indicate that facial expressions might be controlled by a very small number of independent control units, permitting very low-dimensional parametrization of the associated facial expression.

Multiscale Embedded Gene Co-expression Network Analysis

PubMed Central

Song, Won-Min; Zhang, Bin

2015-01-01

Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma. PMID:26618778

Multiscale Embedded Gene Co-expression Network Analysis.

PubMed

Song, Won-Min; Zhang, Bin

2015-11-01

Gene co-expression network analysis has been shown effective in identifying functional co-expressed gene modules associated with complex human diseases. However, existing techniques to construct co-expression networks require some critical prior information such as predefined number of clusters, numerical thresholds for defining co-expression/interaction, or do not naturally reproduce the hallmarks of complex systems such as the scale-free degree distribution of small-worldness. Previously, a graph filtering technique called Planar Maximally Filtered Graph (PMFG) has been applied to many real-world data sets such as financial stock prices and gene expression to extract meaningful and relevant interactions. However, PMFG is not suitable for large-scale genomic data due to several drawbacks, such as the high computation complexity O(|V|3), the presence of false-positives due to the maximal planarity constraint, and the inadequacy of the clustering framework. Here, we developed a new co-expression network analysis framework called Multiscale Embedded Gene Co-expression Network Analysis (MEGENA) by: i) introducing quality control of co-expression similarities, ii) parallelizing embedded network construction, and iii) developing a novel clustering technique to identify multi-scale clustering structures in Planar Filtered Networks (PFNs). We applied MEGENA to a series of simulated data and the gene expression data in breast carcinoma and lung adenocarcinoma from The Cancer Genome Atlas (TCGA). MEGENA showed improved performance over well-established clustering methods and co-expression network construction approaches. MEGENA revealed not only meaningful multi-scale organizations of co-expressed gene clusters but also novel targets in breast carcinoma and lung adenocarcinoma.

Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice

PubMed Central

Chen, Hao; Tang, Yanyan; Liu, Jianfeng; Tan, Lubin; Jiang, Jiahuan; Wang, Mumu; Zhu, Zuofeng; Sun, Xianyou; Sun, Chuanqing

2017-01-01

Grain number is an important factor in determining grain production of rice (Oryza sativa L.). The molecular genetic basis for grain number is complex. Discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. Here, we identified GRAINS NUMBER 2 (GN2), a novel gene that is responsible for rice grain number, from “Yuanjiang” common wild rice (O. rufipogon Griff.). Transgenic plants overexpressing GN2 showed less grain number, reduced plant height, and later heading date than control plants. Interestingly, GN2 arose through the insertion of a 1094-bp sequence from LOC_Os02g45150 into the third exon of LOC_Os02g56630, and the inserted sequence recruited its nearby sequence to generate the chimeric GN2. The gene structure and expression pattern of GN2 were distinct from those of LOC_Os02g45150 and LOC_Os02g56630. Sequence analysis showed that GN2 may be generated in the natural population of Yuanjiang common wild rice. In this study, we identified a novel functional chimeric gene and also provided information regarding the molecular mechanisms regulating rice grain number. PMID:27986805

ALK amplification and protein expression predict inferior prognosis in neuroblastomas.

PubMed

Wang, Miao; Zhou, Chunju; Sun, Qinnuan; Cai, Rongqin; Li, Yong; Wang, Daye; Gong, Liping

2013-10-01

ALK gene has been identified as a major neuroblastoma (NBL) predisposition gene. But ALK gene copy number and protein expression in ganglioneuroblastoma (GNBL) and ganglioneuroma (GN) are poorly described in the literature. Furthermore, there are controversies on the correlation between ALK protein expression and clinical outcome in NBL. We evaluated MYCN/ALK gene copy number by fluorescence in situ hybridization (FISH) and detected ALK protein expression by immunohistochemistry (IHC) in 188 NBL, 52 GNBL and 6 GN samples and analyzed their association with clinical outcome of the patients. Although ALK gene copy number increase is a recurrent genetic aberration of neuroblastic tumors (NTs) (39.1%, 96/246), ALK amplification was only present in three NBLs (1.2%, 3/246). The frequency of ALK positivity in NBL (50.5%, 51/101) was significantly higher than in GNBL (22.6%, 7/31) and in GN (0.0%, 0/4) (P<0.05). In addition, ALK positivity also significantly correlates with MYCN/ALK gene copy number increases (P<0.05). Kaplan-Meier survival analysis indicated that MYCN/ALK amplification is correlated with decreased overall survival in NBL. A better prognosis trend was observed in patients with MYCN/ALK gain tumors compared with those with MYCN/ALK normal tumors. Furthermore, ALK positivity significantly correlated with inferior survival in NBL (P=0.044). ALK positivity in NTs correlated with advanced tumor types and MYCN/ALK gene copy number increases. ALK positivity predicts inferior prognosis in NBL and IHC is a simplified strategy to screen ALK positivity in clinical practice. Copyright © 2013 Elsevier Inc. All rights reserved.

High-Throughput Platform for Patient-Derived, Small Cell Number, Three-Dimensional Ovarian Cancer Spheroids

DTIC Science & Technology

2014-09-01

these small cell number spheroids show 3-D morphology (Figure 3). We also observed differences in the expression of mesenchymal markers when...Scale bar =100 µm. Figure 3: Small cell number spheroids demonstrate 3-D morphology . 3-D reconstructions of confocal z-stacks are shown for...formation was observed with the addition of MSCs, and subsequent co-culture in hanging drop plates preserved spheroid morphology indicated in the phase

Expressing yourself: a feminist analysis of talk around expressing breast milk.

PubMed

Johnson, Sally; Williamson, Iain; Lyttle, Steven; Leeming, Dawn

2009-09-01

Recent feminist analyses, particularly from those working within a poststructuralist framework, have highlighted a number of historically located and contradictory socio-cultural constructions and practices which women are faced with when negotiating infant feeding, especially breastfeeding, within contemporary western contexts. However, there has been little explicit analysis of the practice of expressing breast milk. The aim of this article is to explore the embodied practice of expressing breast milk. This is done by analysing, from a feminist poststructuralist perspective, discourse surrounding expressing breast milk in sixteen first time mothers' accounts of early infant feeding. Participants were recruited from a hospital in the South Midlands of England. The data are drawn from the first phase of a larger longitudinal study, during which mothers kept an audio diary about their breastfeeding experiences for seven days following discharge from hospital, and then took part in a follow-up interview. Key themes identified are expressing breast milk as (i) a way of managing pain whilst still feeding breast milk; (ii) a solution to the inefficiencies of the maternal body; (iii) enhancing or disrupting the 'bonding process'; (iv) a way of managing feeding in public; and (v) a way to negotiate some independence and manage the demands of breastfeeding. Links between these and broader historical and socio-cultural constructions and practices are discussed. This analysis expands current feminist theorising around how women actively create the 'good maternal body'. As constructed by the participants, expressing breast milk appears to be largely a way of aligning subjectivity with cultural ideologies of motherhood. Moreover, breastfeeding discourses and practices available to mothers are not limitless and processes of power restrict the possibilities for women in relation to infant feeding.

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

PubMed

Ramsay, LeeAnn; Marchetto, Maria C; Caron, Maxime; Chen, Shu-Huang; Busche, Stephan; Kwan, Tony; Pastinen, Tomi; Gage, Fred H; Bourque, Guillaume

2017-02-28

A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

Quantifying extrinsic noise in gene expression using the maximum entropy framework.

PubMed

Dixit, Purushottam D

2013-06-18

We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of the gene product (mRNA or protein) by accounting for possible variations in extrinsic factors. The distribution of extrinsic factors is estimated using the maximum entropy principle. Our results show that extrinsic factors qualitatively and quantitatively affect the probability distribution of the gene product. We work out, in detail, the transcription of mRNA from a constitutively expressed promoter in Escherichia coli. We suggest that the variation in extrinsic factors may account for the observed wider-than-Poisson distribution of mRNA copy numbers. We successfully test our framework on a numerical simulation of a simple gene expression scheme that accounts for the variation in extrinsic factors. We also make falsifiable predictions, some of which are tested on previous experiments in E. coli whereas others need verification. Application of the presented framework to more complex situations is also discussed. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Longitudinal waves in a perpendicular collisionless plasma shock. IV - Gradient B.

NASA Technical Reports Server (NTRS)

Gary, S. P.

1972-01-01

The consideration of elastic waves in a Vlasov plasma of unmagnetized ions and magnetized electrons undergoing E x B electron drift and gradient B drift, pursued in the earlier three parts, is brought to conclusion in this last part of the longitudinal wave study in a collisionless plasma shock. Detailed calculations of the effects of the beta sub e dimensionless parameter on the E x B electron drift instability are presented. It is shown that the range of propagation of the elastic waves about the perpendicular remains quite narrow, and that, for oblique propagation, the already narrow angular range of unstable waves is decreased by increases in the value of the beta sub e dimensionless parameter. Also, increases in wave number generally reduce the growth rate and the angular range of propagation.

Energetics of the multi-phase fluid flow in a narrow kerf in laser cutting conditions

NASA Astrophysics Data System (ADS)

Golyshev, A. A.; Orishich, A. M.; Shulyatyev, V. B.

2016-10-01

The energy balance of the multi-phase medium flow is studied experimentally under the laser cutting. Experimental data are generalized due to the condition of minimal roughness of the created surface used as a quality criterion of the melt flow, and also due to the application of dimensionless parameters: Peclet number and dimensionless absorbed laser power. For the first time ever it is found that, regardless the assistant gas (oxygen or nitrogen), laser type (the fiber one with the wavelength of 1.07 µm or CO2-laser with the wavelength of 10.6 µm), the minimal roughness is provided at a certain energy input in a melt unit, about 26 J/mm3. With oxygen, 50% of this input is provided by the radiation, the other 50% - by the exothermic reaction of iron oxidation.

Modelling Problem-Solving Situations into Number Theory Tasks: The Route towards Generalisation

ERIC Educational Resources Information Center

Papadopoulos, Ioannis; Iatridou, Maria

2010-01-01

This paper examines the way two 10th graders cope with a non-standard generalisation problem that involves elementary concepts of number theory (more specifically linear Diophantine equations) in the geometrical context of a rectangle's area. Emphasis is given on how the students' past experience of problem solving (expressed through interplay…

Prognostic Impact of Erythropoietin Expression and Erythropoietin Receptor Expression on Locoregional Control and Survival of Patients Irradiated for Stage II/III Non-Small-Cell Lung Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rades, Dirk, E-mail: Rades.Dirk@gmx.ne; Setter, Cornelia; Dahl, Olav

Purpose: Prognostic factors can guide the physician in selecting the optimal treatment for an individual patient. This study investigates the prognostic value of erythropoietin (EPO) and EPO receptor (EPO-R) expression of tumor cells for locoregional control and survival in non-small-cell lung cancer (NSCLC) patients. Methods and Materials: Fourteen factors were investigated in 62 patients irradiated for stage II/III NSCLC, as follows: age, gender, Karnofsky performance score (KPS), histology, grading, TNM/American Joint Committee on Cancer (AJCC) stage, surgery, chemotherapy, pack years (average number of packages of cigarettes smoked per day multiplied by the number of years smoked), smoking during radiotherapy, hemoglobinmore » levels during radiotherapy, EPO expression, and EPO-R expression. Additionally, patients with tumors expressing both EPO and EPO-R were compared to those expressing either EPO or EPO-R and to those expressing neither EPO nor EPO-R. Results: On univariate analysis, improved locoregional control was associated with AJCC stage II cancer (p < 0.048), surgery (p < 0.042), no smoking during radiotherapy (p = 0.024), and no EPO expression (p = 0.001). A trend was observed for a KPS of >70 (p = 0.08), an N stage of 0 to 1 (p = 0.07), and no EPO-R expression (p = 0.10). On multivariate analysis, AJCC stage II and no EPO expression remained significant. No smoking during radiotherapy was almost significant. On univariate analysis, improved survival was associated with N stage 0 to 1 (p = 0.009), surgery (p = 0.039), hemoglobin levels of {>=}12 g/d (p = 0.016), and no EPO expression (p = 0.001). On multivariate analysis, N stage 0 to 1 and no EPO expression maintained significance. Hemoglobin levels of {>=}12 g/d were almost significant. On subgroup analyses, patients with tumors expressing both EPO and EPO-R had worse outcomes than those expressing either EPO or EPO-R and those expressing neither EPO nor RPO-R. Conclusions: EPO expression of

Ghrelin receptor expression and colocalization with anterior pituitary hormones using a GHSR-GFP mouse line.

PubMed

Reichenbach, Alex; Steyn, Frederik J; Sleeman, Mark W; Andrews, Zane B

2012-11-01

Ghrelin is the endogenous ligand for the GH secretagogue receptor (GHSR) and robustly stimulates GH release from the anterior pituitary gland. Ghrelin also regulates the secretion of anterior pituitary hormones including TSH, LH, prolactin (PRL), and ACTH. However, the relative contribution of a direct action at the GHSR in the anterior pituitary gland vs. an indirect action at the GHSR in the hypothalamus remains undefined. We used a novel GHSR-enhanced green fluorescent protein (eGFP) reporter mouse to quantify GHSR coexpression with GH, TSH, LH, PRL, and ACTH anterior pituitary cells in males vs. females and in chow-fed or calorie-restricted (CR) mice. GHSR-eGFP-expressing cells were only observed in anterior pituitary. The number of GHSR-eGFP-expressing cells was higher in male compared with females, and CR did not affect the GHSR-eGFP cell number. Double staining revealed 77% of somatotrophs expressed GHSR-eGFP in both males and females. Nineteen percent and 12.6% of corticotrophs, 21% and 9% of lactotrophs, 18% and 19% of gonadotrophs, and 3% and 9% of males and females, respectively, expressed GHSR-eGFP. CR increased the number of TSH cells, but suppressed the number of lactotrophs and gonadotrophs, expressing GHSR-eGFP compared with controls. These studies support a robust stimulatory action of ghrelin via the GHSR on GH secretion and identify a previously unknown sexual dimorphism in the GHSR expression in the anterior pituitary. CR affects GHSR-eGFP expression on lactotrophs, gonadotrophs, and thyrotrophs, which may mediate reproductive function and energy metabolism during periods of negative energy balance. The low to moderate expression of GHSR-eGFP suggests that ghrelin plays a minor direct role on remaining anterior pituitary cells.

Hepatic Xenobiotic Metabolizing Enzyme Gene Expression ...

EPA Pesticide Factsheets

BACKGROUND: Differences in responses to environmental chemicals and drugs between life stages are likely due in part to differences in the expression of xenobiotic metabolizing enzymes and transporters (XMETs). No comprehensive analysis of the mRNA expression of XMETs has been carried out through life stages in any species. RESULTS: Using full-genome arrays, the mRNA expression of all XMETs and their regulatory proteins was examined during fetal (gestation day (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND32), middle age (12 months), and old age (18 and 24 months) in the C57BL/6J (C57) mouse liver and compared to adults. Fetal and neonatal life stages exhibited dramatic differences in XMET mRNA expression compared to the relatively minor effects of old age. The total number of XMET probe sets that differed from adults was 636, 500, 84, 5, 43, and 102 for GD19, PND7, PND32, 12 months, 18 months and 24 months, respectively. At all life stages except PND32, under-expressed genes outnumbered over-expressed genes. The altered XMETs included those in all of the major metabolic and transport phases including introduction of reactive or polar groups (Phase I), conjugation (Phase II) and excretion (Phase III). In the fetus and neonate, parallel increases in expression were noted in the dioxin receptor, Nrf2 components and their regulated genes while nuclear receptors and regulated genes were generally down-regulated. Suppression of male-specific XMETs w

Cul4A overexpression associated with Gli1 expression in malignant pleural mesothelioma

DOE PAGES

Yang, Yi -Lin; Ni, Jian; Hsu, Ping -Chih; ...

2015-07-27

Malignant pleural mesothelioma (mesothelioma) is a highly aggressive cancer without an effective treatment. Cul4A, a scaffold protein that recruits substrates for degradation, is amplified in several human cancers, including mesothelioma. We have recently shown that Cul4A plays an oncogenic role in vitro and in a mouse model. In this study, we analysed clinical mesothelioma tumours and found moderate to strong expression of Cul4A in 70.9% (51/72) of these tumours, as shown by immunohistochemistry. In 72.2% mesothelioma tumours with increased Cul4A copy number identified by fluorescence in situ hybridization analysis, Cul4A protein expression was moderate to strong. Similarly, Cul4A was overexpressedmore » and Cul4A copy number was increased in human mesothelioma cell lines. Because Gli1 is highly expressed in human mesothelioma cells, we compared Cul4A and Gli1 expression in mesothelioma tumours and found their expression associated (P < 0.05, chi-square). In mesothelioma cell lines, inhibiting Cul4A by siRNA decreased Gli1 expression, suggesting that Gli1 expression is, at least in part, regulated by Cul4A in mesothelioma cells. Our results suggest a linkage between Cul4A and Gli1 expression in human mesothelioma.« less

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

PubMed

Castle, John C; Biery, Matthew; Bouzek, Heather; Xie, Tao; Chen, Ronghua; Misura, Kira; Jackson, Stuart; Armour, Christopher D; Johnson, Jason M; Rohl, Carol A; Raymond, Christopher K

2010-04-16

DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.

Proliferation, apoptosis and expression of matrix metalloproteinase-9 in human fetal lung.

PubMed

Kraljevic, Daniela; Vukojevic, Katarina; Karan, Dragana; Rajic, Borko; Todorovic, Jelena; Miskovic, Josip; Tomic, Vajdana; Kordic, Mario; Soljic, Violeta

2015-01-01

Expression pattern of the Ki-67, caspase-3 and matrix metalloproteinases-9 (MMP-9) factors were immunohistochemically analyzed in 48 human fetal lungs from 12 to 40 weeks of gestation. The number of Ki-67 positive cells in the epithelium of canaliculare (88cells/mm(2)) and sacculare stage (93cells/mm(2)) were significantly higher than in the epithelium of pseudoglandular stage (12cells/mm(2)) (p=0.0008 vs. p=0.003). The number of Ki-67 positive cells in the mesenchyme of canaliculare stage (132cells/mm(2)) was significantly higher than in the mesenchyme of pseudoglandular stage (37cells/mm(2)) (p=0.001). The proliferation of mesenchymal cells was higher than the epithelial cells in all developmental stages, especially in the canaliculare stage (p=0.007). Similarly, the number of caspase-3 positive cells in the epithelium of canalicular stage (13cells/mm(2)) was significantly higher than in the epithelium of pseudoglandular stage (6cells/mm(2)) (p=0.002) with peaks in the conductive epithelium of canalicular stage. The number of caspase-3 positive cells in the mesenchyme of canaliculare stage (3cells/mm(2)) was significantly higher than in the mesenchyme of saccular stage (0cells/mm(2)) (p=0.05). There were no caspase-3 positive cells in the mesenchyme of pseudoglandular stage. However, unlike the Ki-67 expression, mesenchymal cells in comparison to epithelial cells express substantially less caspase-3 in all developmental stages. Up to the saccular stage, the expression of MMP-9 in mesenchymal cells showed a linear increase with most pronounced expression in that stage. The number of MMP-9 positive cells in the mesenchyme of canaliculare (20cells/mm(2)) and sacculare (39cells/mm(2)) stage were significantly higher than in the mesenchyme of pseudoglandular stage (12cells/mm(2)) (p=0.04 vs. p=0.004). The first epithelial cells that express MMP-9 were present only at the alveolar stage. Increased proliferation and apoptosis of the mesenchymal cells of canalicular

Models of stochastic gene expression

NASA Astrophysics Data System (ADS)

Paulsson, Johan

2005-06-01

Gene expression is an inherently stochastic process: Genes are activated and inactivated by random association and dissociation events, transcription is typically rare, and many proteins are present in low numbers per cell. The last few years have seen an explosion in the stochastic modeling of these processes, predicting protein fluctuations in terms of the frequencies of the probabilistic events. Here I discuss commonalities between theoretical descriptions, focusing on a gene-mRNA-protein model that includes most published studies as special cases. I also show how expression bursts can be explained as simplistic time-averaging, and how generic approximations can allow for concrete interpretations without requiring concrete assumptions. Measures and nomenclature are discussed to some extent and the modeling literature is briefly reviewed.

Magnetic field line random walk in two-dimensional dynamical turbulence

NASA Astrophysics Data System (ADS)

Wang, J. F.; Qin, G.; Ma, Q. M.; Song, T.; Yuan, S. B.

2017-08-01

The field line random walk (FLRW) of magnetic turbulence is one of the important topics in plasma physics and astrophysics. In this article, by using the field line tracing method, the mean square displacement (MSD) of FLRW is calculated on all possible length scales for pure two-dimensional turbulence with the damping dynamical model. We demonstrate that in order to describe FLRW with the damping dynamical model, a new dimensionless quantity R is needed to be introduced. On different length scales, dimensionless MSD shows different relationships with the dimensionless quantity R. Although the temporal effect affects the MSD of FLRW and even changes regimes of FLRW, it does not affect the relationship between the dimensionless MSD and dimensionless quantity R on all possible length scales.

Effects of Forskolin on Trefoil factor 1 expression in cultured ventral mesencephalic dopaminergic neurons.

PubMed

Jensen, P; Ducray, A D; Widmer, H R; Meyer, M

2015-12-03

Trefoil factor 1 (TFF1) belongs to a family of secreted peptides that are mainly expressed in the gastrointestinal tract. Notably, TFF1 has been suggested to operate as a neuropeptide, however, its specific cellular expression, regulation and function remain largely unknown. We have previously shown that TFF1 is expressed in developing and adult rat ventral mesencephalic tyrosine hydroxylase-immunoreactive (TH-ir) dopaminergic neurons. Here, we investigated the expression of TFF1 in rat ventral mesencephalic dopaminergic neurons (embryonic day 14) grown in culture for 5, 7 or 10 days in the absence (controls) or presence of either glial cell line-derived neurotrophic factor (GDNF), Forskolin or the combination. No TFF1-ir cells were identified at day 5 and only a few at day 7, whereas TH was markedly expressed at both time points. At day 10, several TFF1-ir cells were detected, and their numbers were significantly increased after the addition of GDNF (2.2-fold) or Forskolin (4.1-fold) compared to controls. Furthermore, the combination of GDNF and Forskolin had an additive effect and increased the number of TFF1-ir cells by 5.6-fold compared to controls. TFF1 expression was restricted to neuronal cells, and the percentage of TH/TFF1 co-expressing cells was increased to the same extent in GDNF and Forskolin-treated cultures (4-fold) as compared to controls. Interestingly, the combination of GDNF and Forskolin resulted in a significantly increased co-expression (8-fold) of TH/TFF1, which could indicate that GDNF and Forskolin targeted different subpopulations of TH/TFF1 neurons. Short-term treatment with Forskolin resulted in an increased number of TFF1-ir cells, and this effect was significantly reduced by the MEK1 inhibitor PD98059 or the protein kinase A (PKA) inhibitor H89, suggesting that Forskolin induced TFF1 expression through diverse signaling pathways. In conclusion, distinct populations of cultured dopaminergic neurons express TFF1, and their numbers can be

Inferring causal genomic alterations in breast cancer using gene expression data

PubMed Central

2011-01-01

Background One of the primary objectives in cancer research is to identify causal genomic alterations, such as somatic copy number variation (CNV) and somatic mutations, during tumor development. Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of these studies. Results We developed a framework for identifying recurrent regions of CNV and distinguishing the cancer driver genes from the passenger genes in the regions. By inferring CNV regions across many datasets we were able to identify 109 recurrent amplified/deleted CNV regions. Many of these regions are enriched for genes involved in many important processes associated with tumorigenesis and cancer progression. Genes in these recurrent CNV regions were then examined in the context of gene regulatory networks to prioritize putative cancer driver genes. The cancer driver genes uncovered by the framework include not only well-known oncogenes but also a number of novel cancer susceptibility genes validated via siRNA experiments. Conclusions To our knowledge, this is the first effort to systematically identify and validate drivers for expression based CNV regions in breast cancer. The framework where the wavelet analysis of copy number alteration based on expression coupled with the gene regulatory network analysis, provides a blueprint for leveraging genomic data to identify key regulatory components and gene targets. This integrative approach can be applied to many other large-scale gene expression studies and other novel types of cancer data such as next-generation sequencing based expression (RNA-Seq) as well as CNV data. PMID:21806811

Geometry and starvation effects in hydrodynamic lubrication

NASA Technical Reports Server (NTRS)

Brewe, D.; Hamrock, B. J.

1982-01-01

Numerical methods were used to detemine the effects of lubricant starvation on the minimum film thickness under conditions of a hydrodynamic point contact. Starvation was effected by varying the fluid inlet level. The Reynolds boundary conditions were applied at the cavitation boundary and zero pressure was stipulated at the meniscus or inlet boundary. A minimum film thickness equation as a function of both the ratio of dimensionless load to dimensionless speed and inlet supply level was determined. By comparing the film generated under the starved inlet condition with the film generated from the fully flooded inlet, an expression for the film reduction factor was obtained. Based on this factor a starvation threshold was defined as well as a critically starved inlet. The changes in the inlet pressure buildup due to changing the available lubricant supply are presented in the form of three dimensional isometric plots and also in the form of contour plots.

Analysis of starvation effects on hydrodynamic lubrication in nonconforming contacts

NASA Technical Reports Server (NTRS)

Brewe, D. E.; Hamrock, B. J.

1981-01-01

The effects of lubricant starvation on minimum film thickness, under conditions of a hydrodynamic point contact, are determined by numerical methods where: (1) starvation is effected by varying the fluid inlet level; (2) the Reynolds boundary conditions are applied at the cavitation boundary; and (3) zero pressure is stipulated at the meniscus or inlet boundary. Seventy-four cases were used to numerically determine a minimum-film-thickness equation, as a function of the ratio of dimensionless load to dimensionless speed for varying degrees of starvation. A film reduction factor was in turn determined as a function of the fluid inlet level, and a starved, fully-flooded boundary was defined along with an expression determining the onset of starvation. It is found that as the degree of starvation increases, the minimum film thickness decreases gradually until the fluid inlet becomes critical. The changes in the inlet pressure buildup due to changing the available lubricant supply are presented in the form of three-dimensional isometric plots.

Analysis of starvation effects on hydrodynamic lubrication in nonconforming contacts

NASA Technical Reports Server (NTRS)

Brewe, D. E.; Hamrock, B. J.

1981-01-01

Numerical methods were used to determine the effects of lubricant starvation on the minimum film thickness under conditions of a hydrodynamic point contact. Starvation was effected by varying the fluid inlet level. The Reynolds boundary conditions were applied at the cavitation boundary and zero pressure was stipulated at the meniscus or inlet boundary. A minimum-fill-thickness equation as a function of both the ratio of dimensionless load to dimensionless speed and inlet supply level was determined. By comparing the film generated under the starved inlet condition with the film generated from the fully flooded inlet, an expression for the film reduction factor was obtained. Based on this factor a starvation threshold was defined as well as a critically starved inlet. The changes in the inlet pressure buildup due to changing the available lubricant supply are presented in the form of three dimensional isometric plots and also in the form of contour plots.

Geometry and starvation effects in hydrodynamic lubrication

NASA Technical Reports Server (NTRS)

Brewe, D. E.; Hamrock, B. J.

1982-01-01

Numerical methods were used to determine the effects of lubricant starvation on the minimum film thickness under conditions of a hydrodynamic point contact. Starvation was effected by varying the fluid inlet level. The Reynolds boundary conditions were applied at the cavitation boundary and zero pressure was stipulated at the meniscus or inlet boundary. A minimum-film-thickness equation as a function of both the ratio of dimensionless load to dimensionless speed and inlet supply level was determined. By comparing the film generated under the starved inlet condition with the film generated from the fully flooded inlet, an expression for the film reduction factor was obtained. Based on this factor a starvation threshold was defined as well as a critically starved inlet. The changes in the inlet pressure buildup due to changing the available lubricant supply are presented in the form of three dimensional isometric plots and also in the form of contour plots.

Automated Discovery of Functional Generality of Human Gene Expression Programs

PubMed Central

Gerber, Georg K; Dowell, Robin D; Jaakkola, Tommi S; Gifford, David K

2007-01-01

An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional breadth of these programs. The use of human expression data compendia for discovery of such programs presents several challenges including cellular inhomogeneity within samples, genetic and environmental variation across samples, uncertainty in the numbers of programs and sample populations, and temporal behavior. We developed GeneProgram, a new unsupervised computational framework based on Hierarchical Dirichlet Processes that addresses each of the above challenges. GeneProgram uses expression data to simultaneously organize tissues into groups and genes into overlapping programs with consistent temporal behavior, to produce maps of expression programs, which are sorted by generality scores that exploit the automatically learned groupings. Using synthetic and real gene expression data, we showed that GeneProgram outperformed several popular expression analysis methods. We applied GeneProgram to a compendium of 62 short time-series gene expression datasets exploring the responses of human cells to infectious agents and immune-modulating molecules. GeneProgram produced a map of 104 expression programs, a substantial number of which were significantly enriched for genes involved in key signaling pathways and/or bound by NF-κB transcription factors in genome-wide experiments. Further, GeneProgram discovered expression programs that appear to implicate surprising signaling pathways or receptor types in the response to infection, including Wnt signaling and neurotransmitter receptors. We believe the discovered map of expression programs involved in the response to infection will be useful for guiding future biological experiments; genes from programs with low generality scores might serve as new drug targets that exhibit minimal “cross-talk,” and

A high-throughput microRNA expression profiling system.

PubMed

Guo, Yanwen; Mastriano, Stephen; Lu, Jun

2014-01-01

As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.

Beyond Natural Numbers: Negative Number Representation in Parietal Cortex

PubMed Central

Blair, Kristen P.; Rosenberg-Lee, Miriam; Tsang, Jessica M.; Schwartz, Daniel L.; Menon, Vinod

2012-01-01

Unlike natural numbers, negative numbers do not have natural physical referents. How does the brain represent such abstract mathematical concepts? Two competing hypotheses regarding representational systems for negative numbers are a rule-based model, in which symbolic rules are applied to negative numbers to translate them into positive numbers when assessing magnitudes, and an expanded magnitude model, in which negative numbers have a distinct magnitude representation. Using an event-related functional magnetic resonance imaging design, we examined brain responses in 22 adults while they performed magnitude comparisons of negative and positive numbers that were quantitatively near (difference <4) or far apart (difference >6). Reaction times (RTs) for negative numbers were slower than positive numbers, and both showed a distance effect whereby near pairs took longer to compare. A network of parietal, frontal, and occipital regions were differentially engaged by negative numbers. Specifically, compared to positive numbers, negative number processing resulted in greater activation bilaterally in intraparietal sulcus (IPS), middle frontal gyrus, and inferior lateral occipital cortex. Representational similarity analysis revealed that neural responses in the IPS were more differentiated among positive numbers than among negative numbers, and greater differentiation among negative numbers was associated with faster RTs. Our findings indicate that despite negative numbers engaging the IPS more strongly, the underlying neural representation are less distinct than that of positive numbers. We discuss our findings in the context of the two theoretical models of negative number processing and demonstrate how multivariate approaches can provide novel insights into abstract number representation. PMID:22363276

Beyond natural numbers: negative number representation in parietal cortex.

PubMed

Blair, Kristen P; Rosenberg-Lee, Miriam; Tsang, Jessica M; Schwartz, Daniel L; Menon, Vinod

2012-01-01

Unlike natural numbers, negative numbers do not have natural physical referents. How does the brain represent such abstract mathematical concepts? Two competing hypotheses regarding representational systems for negative numbers are a rule-based model, in which symbolic rules are applied to negative numbers to translate them into positive numbers when assessing magnitudes, and an expanded magnitude model, in which negative numbers have a distinct magnitude representation. Using an event-related functional magnetic resonance imaging design, we examined brain responses in 22 adults while they performed magnitude comparisons of negative and positive numbers that were quantitatively near (difference <4) or far apart (difference >6). Reaction times (RTs) for negative numbers were slower than positive numbers, and both showed a distance effect whereby near pairs took longer to compare. A network of parietal, frontal, and occipital regions were differentially engaged by negative numbers. Specifically, compared to positive numbers, negative number processing resulted in greater activation bilaterally in intraparietal sulcus (IPS), middle frontal gyrus, and inferior lateral occipital cortex. Representational similarity analysis revealed that neural responses in the IPS were more differentiated among positive numbers than among negative numbers, and greater differentiation among negative numbers was associated with faster RTs. Our findings indicate that despite negative numbers engaging the IPS more strongly, the underlying neural representation are less distinct than that of positive numbers. We discuss our findings in the context of the two theoretical models of negative number processing and demonstrate how multivariate approaches can provide novel insights into abstract number representation.

Progression of renal fibrosis in congenital CKD model rats with reduced number of nephrons.

PubMed

Yasuda, Hidenori; Tochigi, Yuki; Katayama, Kentaro; Suzuki, Hiroetsu

2017-06-14

A congenital reduction in the number of nephrons is a critical risk factor for both onset of chronic kidney disease (CKD) and its progression to end-stage kidney disease (ESKD). Hypoplastic kidney (HPK) rats have only about 20% of the normal number of nephrons and show progressive CKD. This study used an immunohistological method to assess glomerular and interstitial pathogenesis in male HPK rats aged 35-210days. CD68 positive-macrophages were found to infiltrate into glomeruli in HPK rats aged 35 and 70days and to infiltrate into interstitial tissue in rats aged 140 and 210days. HPK rats aged 35 and 70days showed glomerular hypertrophy, loss of normal linear immunostaining of podocine, and increased expression of PDGFr-β, TGF-β, collagens, and fibronectin, with all of these alterations gradually deteriorating with age. α-SMA-positive myofibroblasts were rarely detected in glomerular tufts, whereas α-SMA-positive glomerular parietal epithelium (GPE) cells were frequently observed along Bowman's capsular walls. The numbers of PDGFr-β-positive fibroblasts in interstitial tissue were increased in rats aged 35days and older, whereas interstitial fibrosis, characterized by the increased expression of tubular PDGF-BB, the appearance of myofibroblasts doubly positive for PDGFr-β and α-SMA, and increased expression of collagens and fibronectin, were observed in rats aged 70 and older. These results clearly indicate that congenital CKD with only 20% of nephrons cause renal fibrosis in rats. Copyright © 2017 Elsevier GmbH. All rights reserved.

Different approach to the modeling of nonfree particle diffusion

NASA Astrophysics Data System (ADS)

Buhl, Niels

2018-03-01

A new approach to the modeling of nonfree particle diffusion is presented. The approach uses a general setup based on geometric graphs (networks of curves), which means that particle diffusion in anything from arrays of barriers and pore networks to general geometric domains can be considered and that the (free random walk) central limit theorem can be generalized to cover also the nonfree case. The latter gives rise to a continuum-limit description of the diffusive motion where the effect of partially absorbing barriers is accounted for in a natural and non-Markovian way that, in contrast to the traditional approach, quantifies the absorptivity of a barrier in terms of a dimensionless parameter in the range 0 to 1. The generalized theorem gives two general analytic expressions for the continuum-limit propagator: an infinite sum of Gaussians and an infinite sum of plane waves. These expressions entail the known method-of-images and Laplace eigenfunction expansions as special cases and show how the presence of partially absorbing barriers can lead to phenomena such as line splitting and band gap formation in the plane wave wave-number spectrum.

Relaxation of an unsteady turbulent boundary layer on a flat plate in an expansion tube

NASA Technical Reports Server (NTRS)

Gurta, R. N.; Trimpi, R. L.

1974-01-01

An analysis is presented for the relaxation of a turbulent boundary layer on a semi-infinite flat plate after passage of a shock wave and a trailing driver gas-driven gas interface. The problem has special application to expansion-tube flows. The flow-governing equations have been transformed into the Crocco variables, and a time-similar solution is presented in terms of the dimensionless distance-time variable alpha and the dimensionless velocity variable beta. An eddy-viscosity model, similar to that of time-steady boundary layers, is applied to the inner and outer regions of the boundary layer. A turbulent Prandtl number equal to the molecular Prandtl number is used to relate the turbulent heat flux to the eddy viscosity. The numerical results, obtained by using the Gauss-Seidel line-relaxation method, indicate that a fully turbulent boundary layer relaxes faster to the final steady-state values of heat transfer and skin friction than a laminar boundary layer. The results also give a fairly good estimate of the local skin friction and heat transfer for near steady-flow conditions.

Hydrodynamic structure of the boundary layers in a rotating cylindrical cavity with radial inflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herrmann-Priesnitz, Benjamín, E-mail: bherrman@ing.uchile.cl; Torres, Diego A.; Advanced Mining Technology Center, Universidad de Chile, Av. Tupper 2007, Santiago

A flow model is formulated to investigate the hydrodynamic structure of the boundary layers of incompressible fluid in a rotating cylindrical cavity with steady radial inflow. The model considers mass and momentum transfer coupled between boundary layers and an inviscid core region. Dimensionless equations of motion are solved using integral methods and a space-marching technique. As the fluid moves radially inward, entraining boundary layers develop which can either meet or become non-entraining. Pressure and wall shear stress distributions, as well as velocity profiles predicted by the model, are compared to numerical simulations using the software OpenFOAM. Hydrodynamic structure of themore » boundary layers is governed by a Reynolds number, Re, a Rossby number, Ro, and the dimensionless radial velocity component at the periphery of the cavity, U{sub o}. Results show that boundary layers merge for Re < < 10 and Ro > > 0.1, and boundary layers become predominantly non-entraining for low Ro, low Re, and high U{sub o}. Results may contribute to improve the design of technology, such as heat exchange devices, and turbomachinery.« less

Mathematical Model of the Processes of Heat and Mass Transfer and Diffusion of the Magnetic Field in an Induction Furnace

NASA Astrophysics Data System (ADS)

Perminov, A. V.; Nikulin, I. L.

2016-03-01

We propose a mathematical model describing the motion of a metal melt in a variable inhomogeneous magnetic field of a short solenoid. In formulating the problem, we made estimates and showed the possibility of splitting the complete magnetohydrodynamical problem into two subproblems: a magnetic field diffusion problem where the distributions of the external and induced magnetic fields and currents are determined, and a heat and mass transfer problem with known distributions of volume sources of heat and forces. The dimensionless form of the heat and mass transfer equation was obtained with the use of averaging and multiscale methods, which permitted writing and solving separately the equations for averaged flows and temperature fields and their oscillations. For the heat and mass transfer problem, the boundary conditions for a real technological facility are discussed. The dimensionless form of the magnetic field diffusion equation is presented, and the experimental computational procedure and results of the numerical simulation of the magnetic field structure in the melt for various magnetic Reynolds numbers are described. The extreme dependence of heat release on the magnetic Reynolds number has been interpreted.

Quantification of free convection effects on 1 kg mass standards

NASA Astrophysics Data System (ADS)

Schreiber, M.; Emran, M. S.; Fröhlich, T.; Schumacher, J.; Thess, A.

2015-12-01

We determine the free-convection effects and the resulting mass differences in a high-precision mass comparator for cylindrical and spherical 1 kg mass standards at different air pressures. The temperature differences are chosen in the millikelvin range and lead to microgram updrafts. Our studies reveal a good agreement between the measurements and direct numerical simulations of the Boussinesq equations of free thermal convection. A higher sensitivity to the free convection effects is found for the spherical case compared to the cylindrical one. We also translate our results on the free convection effects into a form which is used in fluid mechanics: a dimensionless updraft coefficient as a function of the dimensionless Grashof number Gr that quantifies the thermal driving due to temperature differences. This relation displays a unique scaling behavior over nearly four decades in Gr and levels off into geometry-specific constants for the very small Grashof numbers. The obtained results provide a rational framework for estimating systematic errors in mass metrology due to the effects of free convection.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

PubMed

Keates, Tracy; Cooper, Christopher D O; Savitsky, Pavel; Allerston, Charles K; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-06-15

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. Copyright © 2011 Elsevier B.V. All rights reserved.

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

PubMed Central

Keates, Tracy; Cooper, Christopher D.O.; Savitsky, Pavel; Allerston, Charles K.; Phillips, Claire; Hammarström, Martin; Daga, Neha; Berridge, Georgina; Mahajan, Pravin; Burgess-Brown, Nicola A.; Müller, Susanne; Gräslund, Susanne; Gileadi, Opher

2012-01-01

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome. PMID:22027370

A simplified Mach number scaling law for helicopter rotor noise

NASA Technical Reports Server (NTRS)

Aravamudan, K. S.; Lee, A.; Harris, W. L.

1978-01-01

Mach number scaling laws are derived for the rotational and the high-frequency broadband noise from helicopter rotors. The rotational scaling law is obtained directly from the theory of Lowson and Ollerhead (1969) by exploiting the properties of the dominant terms in the expression for the complex Fourier coefficients of sound radiation from a point source. The scaling law for the high-frequency broadband noise is obtained by assuming that the noise sources are acoustically compact and computing the instantaneous pressure due to an element on an airfoil where vortices are shed. Experimental results on the correlation lengths for stationary airfoils are extended to rotating airfoils. On the assumption that the correlation length varies as the boundary layer displacement thickness, it is found that the Mach number scaling law contains a factor of Mach number raised to the exponent 5.8. Both scaling laws were verified by model tests.

The Mental Number Line in Dyscalculia: Impaired Number Sense or Access from Symbolic Numbers?

ERIC Educational Resources Information Center

Lafay, Anne; St-Pierre, Marie-Catherine; Macoir, Joël

2017-01-01

Numbers may be manipulated and represented mentally over a compressible number line oriented from left to right. According to numerous studies, one of the primary reasons for dyscalculia is related to improper understanding of the mental number line. Children with dyscalculia usually show difficulty when they have to place Arabic numbers on a…

COX-2 expression positively correlates with PD-L1 expression in human melanoma cells.

PubMed

Botti, Gerardo; Fratangelo, Federica; Cerrone, Margherita; Liguori, Giuseppina; Cantile, Monica; Anniciello, Anna Maria; Scala, Stefania; D'Alterio, Crescenzo; Trimarco, Chiara; Ianaro, Angela; Cirino, Giuseppe; Caracò, Corrado; Colombino, Maria; Palmieri, Giuseppe; Pepe, Stefano; Ascierto, Paolo Antonio; Sabbatino, Francesco; Scognamiglio, Giosuè

2017-02-23

The resistance to PD-1/PD-L1 inhibitors for the treatment of melanoma have prompted investigators to implement novel clinical trials which combine immunotherapy with different treatment modalities. Moreover is also important to investigate the mechanisms which regulate the dynamic expression of PD-L1 on tumor cells and PD-1 on T cells in order to identify predictive biomarkers of response. COX-2 is currently investigated as a major player of tumor progression in several type of malignancies including melanoma. In the present study we investigated the potential relationship between COX-2 and PD-L1 expression in melanoma. Tumor samples obtained from primary melanoma lesions and not matched lymph node metastases were analyzed for both PD-L1 and COX-2 expression by IHC analysis. Status of BRAF and NRAS mutations was analyzed by sequencing and PCR. Co-localization of PD-L1 and COX-2 expression was analyzed by double fluorescence staining. Lastly the BRAF V600E A375 and NRAS Q61R SK-MEL-2 melanoma cell lines were used to evaluate the effect of COX-2 inhibition by celecoxib on expression of PD-L1 in vitro. BRAF V600E/V600K and NRAS Q61R/Q61L were detected in 57.8 and 8.9% of the metastatic lesions, and in 65.9 and 6.8% of the primary tumors, respectively. PD-L1 and COX-2 expression were heterogeneously expressed in both primary melanoma lesions and not matched lymph node metastases. A significantly lower number of PD-L1 negative lesions was found in primary tumors as compared to not matched metastatic lesions (P = 0.002). COX-2 expression significantly correlated with PD-L1 expression in both primary (P = 0.001) and not matched metastatic (P = 0.048) lesions. Furthermore, in melanoma tumors, cancer cells expressing a higher levels of COX-2 also co-expressed a higher level of PD-L1. Lastly, inhibition of COX-2 activity by celecoxib down-regulated the expression of PD-L1 in both BRAF V600E A375 and NRAS Q61R SK-MEL-2 melanoma cell lines. COX-2 expression correlates

Microarray expression profiling and co-expression network analysis of circulating LncRNAs and mRNAs associated with neurotoxicity induced by BPA.

PubMed

Pang, Wei; Lian, Fu-Zhi; Leng, Xue; Wang, Shu-Min; Li, Yi-Bo; Wang, Zi-Yu; Li, Kai-Ren; Gao, Zhi-Xian; Jiang, Yu-Gang

2018-05-01

A growing body of evidence has shown bisphenol A (BPA), an estrogen-like industrial chemical, has adverse effects on the nervous system. In this study, we investigated the transcriptional behavior of long non-coding RNAs (lncRNAs) and mRNAs to provide the information to explore neurotoxic effects induced by BPA. By microarray expression profiling, we discovered 151 differentially expressed lncRNAs and 794 differentially expressed mRNAs in the BPA intervention group compared with the control group. Gene ontology analysis indicated the differentially expressed mRNAs were mainly involved in fundamental metabolic processes and physiological and pathological conditions, such as development, synaptic transmission, homeostasis, injury, and neuroinflammation responses. In the expression network of the BPA-induced group, a great number of nodes and connections were found in comparison to the control-derived network. We identified lncRNAs that were aberrantly expressed in the BPA group, among which, growth arrest specific 5 (GAS5) might participate in the BPA-induced neurotoxicity by regulating Jun, RAS, and other pathways indirectly through these differentially expressed genes. This study provides the first investigation of genome-wide lncRNA expression and correlation between lncRNA and mRNA expression in the BPA-induced neurotoxicity. Our results suggest that the elevated expression of lncRNAs is a major biomarker in the neurotoxicity induced by BPA.

Expression and rearrangement of the ROS1 gene in human glioblastoma cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Birchmeier, C.; Sharma, S.; Wigler, M.

1987-12-01

The human ROS1 gene, which possibly encodes a growth factor receptor, was found to be expressed in human tumor cell lines. In a survey of 45 different human cell lines, the authors found ROS1 to be expressed in glioblastoma-derived cell lines at high levels and not to be expressed at all, or expressed at very low levels, in the remaining cell lines. The ROS1 gene was present in normal copy numbers in all cell lines that expressed the gene. However, in one particular glioblastoma line, they detected a potentially activating mutation at the ROS1 locus.

Individual Differences in Algebraic Cognition: Relation to the Approximate Number and Sematic Memory Systems

PubMed Central

Geary, David C.; Hoard, Mary K.; Nugent, Lara; Rouder, Jeffrey N.

2015-01-01

The relation between performance on measures of algebraic cognition and acuity of the approximate number system (ANS) and memory for addition facts was assessed for 171 (92 girls) 9th graders, controlling parental education, sex, reading achievement, speed of numeral processing, fluency of symbolic number processing, intelligence, and the central executive component of working memory. The algebraic tasks assessed accuracy in placing x,y pairs in the coordinate plane, speed and accuracy of expression evaluation, and schema memory for algebra equations. ANS acuity was related to accuracy of placements in the coordinate plane and expression evaluation, but not schema memory. Frequency of fact-retrieval errors was related to schema memory but not coordinate plane or expression evaluation accuracy. The results suggest the ANS may contribute to or is influenced by spatial-numerical and numerical only quantity judgments in algebraic contexts, whereas difficulties in committing addition facts to long-term memory may presage slow formation of memories for the basic structure of algebra equations. More generally, the results suggest different brain and cognitive systems are engaged during the learning of different components of algebraic competence, controlling demographic and domain general abilities. PMID:26255604

[Expression and clinical significance of KIAA1199 in primary hepatocellular carcinoma].

PubMed

Gu, C J; Ni, Q C; Ni, K; Zhang, S; Qian, H X

2018-05-29

Objective: To investigate the expression and clinical significance of KIAA1199 in primary hepatocellular carcinoma. Methods: A total of 136 cases of primary hepatocellular carcinoma tissues and paired adjacent tissues were collected. Immunohistochemistry and Western blot were used to detect the expression of KIAA1199 in primary hepatocellular carcinoma tissues and paired adjacent tissues. The relationship between KIAA1199 and clinicopathological parameter of primary hepatocellular carcinoma was analyzed. Results: The positive rate of KIAA1199 in primary hepatocellular carcinoma was 82.3% (112/136), which was higher than that in paired para-cancerous tissues (14.7%, 20/136). High expression of KIAA1199 was significantly correlated with age, cirrhosis history, tumor size, tumor number, degree of differentiation, TNM staging and microvenous invasion (MVI) ( P <0.05), but without gender, drinking alcohol hobby, hepatitis history, family genetic history, tumor location ( P >0.05). The Kaplan-Meier survival curves indicated that high KIAA1199 expression was associated with poor survival ( P <0.01). In addition, Cox proportional hazards model showed that the expression of KIAA1199 was related to age, cirrhosis history, tumor size, tumor number, degree of differentiation, TNM staging and MVI ( P <0.05). Conclusion: The expression of KIAA1199 is up-regulated in primary hepatocellular carcinoma, which is significantly correlated with the clinicopathological features and prognosis, high expression of KIAA1199 increased the risk of death in patients with primary hepatocellular carcinoma.

Froude number fractions to increase walking pattern dynamic similarities: application to plantar pressure study in healthy subjects.